docker run -p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:/owl_web -v /Users/sam/gitrepos:/gitrepos -it f99537d7e06a
The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.
Once the container was started, started Jupyter Notebook with the following command inside the Docker container:
jupyter notebook
This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.
The Docker container is running on an image created from this Dockerfile (Git commit 443bc42)
%%bash
date
Mon Mar 6 16:47:23 UTC 2017
%%bash
hostname
0f2bca9c664b
%%bash
lscpu
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 8 On-line CPU(s) list: 0-7 Thread(s) per core: 1 Core(s) per socket: 8 Socket(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 26 Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz Stepping: 5 CPU MHz: 2260.998 BogoMIPS: 4521.99 Hypervisor vendor: KVM Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 8192K
ls /owl_web/nightingales/O_lurida/20160223_gbs/
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/ 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/ 1HL_10A_1.fq.gz* 1HL_10A_2.fq.gz* 1HL_11A_1.fq.gz* 1HL_11A_2.fq.gz* 1HL_12A_1.fq.gz* 1HL_12A_2.fq.gz* 1HL_13A_1.fq.gz* 1HL_13A_2.fq.gz* 1HL_14A_1.fq.gz* 1HL_14A_2.fq.gz* 1HL_15A_1.fq.gz* 1HL_15A_2.fq.gz* 1HL_16A_1.fq.gz* 1HL_16A_2.fq.gz* 1HL_17A_1.fq.gz* 1HL_17A_2.fq.gz* 1HL_19A_1.fq.gz* 1HL_19A_2.fq.gz* 1HL_1A_1.fq.gz* 1HL_1A_2.fq.gz* 1HL_20A_1.fq.gz* 1HL_20A_2.fq.gz* 1HL_21A_1.fq.gz* 1HL_21A_2.fq.gz* 1HL_22A_1.fq.gz* 1HL_22A_2.fq.gz* 1HL_23A_1.fq.gz* 1HL_23A_2.fq.gz* 1HL_24A_1.fq.gz* 1HL_24A_2.fq.gz* 1HL_25A_1.fq.gz* 1HL_25A_2.fq.gz* 1HL_26A_1.fq.gz* 1HL_26A_2.fq.gz* 1HL_27A_1.fq.gz* 1HL_27A_2.fq.gz* 1HL_28A_1.fq.gz* 1HL_28A_2.fq.gz* 1HL_29A_1.fq.gz* 1HL_29A_2.fq.gz* 1HL_2A_1.fq.gz* 1HL_2A_2.fq.gz* 1HL_31A_1.fq.gz* 1HL_31A_2.fq.gz* 1HL_33A_1.fq.gz* 1HL_33A_2.fq.gz* 1HL_34A_1.fq.gz* 1HL_34A_2.fq.gz* 1HL_35A_1.fq.gz* 1HL_35A_2.fq.gz* 1HL_3A_1.fq.gz* 1HL_3A_2.fq.gz* 1HL_4A_1.fq.gz* 1HL_4A_2.fq.gz* 1HL_5A_1.fq.gz* 1HL_5A_2.fq.gz* 1HL_6A_1.fq.gz* 1HL_6A_2.fq.gz* 1HL_7A_1.fq.gz* 1HL_7A_2.fq.gz* 1HL_8A_1.fq.gz* 1HL_8A_2.fq.gz* 1HL_9A_1.fq.gz* 1HL_9A_2.fq.gz* 1NF_10A_1.fq.gz* 1NF_10A_2.fq.gz* 1NF_11A_1.fq.gz* 1NF_11A_2.fq.gz* 1NF_12A_1.fq.gz* 1NF_12A_2.fq.gz* 1NF_13A_1.fq.gz* 1NF_13A_2.fq.gz* 1NF_14A_1.fq.gz* 1NF_14A_2.fq.gz* 1NF_15A_1.fq.gz* 1NF_15A_2.fq.gz* 1NF_16A_1.fq.gz* 1NF_16A_2.fq.gz* 1NF_17A_1.fq.gz* 1NF_17A_2.fq.gz* 1NF_18A_1.fq.gz* 1NF_18A_2.fq.gz* 1NF_19A_1.fq.gz* 1NF_19A_2.fq.gz* 1NF_1A_1.fq.gz* 1NF_1A_2.fq.gz* 1NF_20A_1.fq.gz* 1NF_20A_2.fq.gz* 1NF_21A_1.fq.gz* 1NF_21A_2.fq.gz* 1NF_22A_1.fq.gz* 1NF_22A_2.fq.gz* 1NF_23A_1.fq.gz* 1NF_23A_2.fq.gz* 1NF_24A_1.fq.gz* 1NF_24A_2.fq.gz* 1NF_25A_1.fq.gz* 1NF_25A_2.fq.gz* 1NF_26A_1.fq.gz* 1NF_26A_2.fq.gz* 1NF_27A_1.fq.gz* 1NF_27A_2.fq.gz* 1NF_28A_1.fq.gz* 1NF_28A_2.fq.gz* 1NF_29A_1.fq.gz* 1NF_29A_2.fq.gz* 1NF_2A_1.fq.gz* 1NF_2A_2.fq.gz* 1NF_30A_1.fq.gz* 1NF_30A_2.fq.gz* 1NF_31A_1.fq.gz* 1NF_31A_2.fq.gz* 1NF_32A_1.fq.gz* 1NF_32A_2.fq.gz* 1NF_33A_1.fq.gz* 1NF_33A_2.fq.gz* 1NF_4A_1.fq.gz* 1NF_4A_2.fq.gz* 1NF_5A_1.fq.gz* 1NF_5A_2.fq.gz* 1NF_6A_1.fq.gz* 1NF_6A_2.fq.gz* 1NF_7A_1.fq.gz* 1NF_7A_2.fq.gz* 1NF_8A_1.fq.gz* 1NF_8A_2.fq.gz* 1NF_9A_1.fq.gz* 1NF_9A_2.fq.gz* 1SN_10A_1.fq.gz* 1SN_10A_2.fq.gz* 1SN_11A_1.fq.gz* 1SN_11A_2.fq.gz* 1SN_12A_1.fq.gz* 1SN_12A_2.fq.gz* 1SN_13A_1.fq.gz* 1SN_13A_2.fq.gz* 1SN_14A_1.fq.gz* 1SN_14A_2.fq.gz* 1SN_15A_1.fq.gz* 1SN_15A_2.fq.gz* 1SN_16A_1.fq.gz* 1SN_16A_2.fq.gz* 1SN_17A_1.fq.gz* 1SN_17A_2.fq.gz* 1SN_18A_1.fq.gz* 1SN_18A_2.fq.gz* 1SN_19A_1.fq.gz* 1SN_19A_2.fq.gz* 1SN_1A_1.fq.gz* 1SN_1A_2.fq.gz* 1SN_20A_1.fq.gz* 1SN_20A_2.fq.gz* 1SN_21A_1.fq.gz* 1SN_21A_2.fq.gz* 1SN_22A_1.fq.gz* 1SN_22A_2.fq.gz* 1SN_23A_1.fq.gz* 1SN_23A_2.fq.gz* 1SN_24A_1.fq.gz* 1SN_24A_2.fq.gz* 1SN_25A_1.fq.gz* 1SN_25A_2.fq.gz* 1SN_26A_1.fq.gz* 1SN_26A_2.fq.gz* 1SN_27A_1.fq.gz* 1SN_27A_2.fq.gz* 1SN_28A_1.fq.gz* 1SN_28A_2.fq.gz* 1SN_29A_1.fq.gz* 1SN_29A_2.fq.gz* 1SN_2A_1.fq.gz* 1SN_2A_2.fq.gz* 1SN_30A_1.fq.gz* 1SN_30A_2.fq.gz* 1SN_31A_1.fq.gz* 1SN_31A_2.fq.gz* 1SN_32A_1.fq.gz* 1SN_32A_2.fq.gz* 1SN_3A_1.fq.gz* 1SN_3A_2.fq.gz* 1SN_4A_1.fq.gz* 1SN_4A_2.fq.gz* 1SN_5A_1.fq.gz* 1SN_5A_2.fq.gz* 1SN_6A_1.fq.gz* 1SN_6A_2.fq.gz* 1SN_7A_1.fq.gz* 1SN_7A_2.fq.gz* 1SN_8A_1.fq.gz* 1SN_8A_2.fq.gz* 1SN_9A_1.fq.gz* 1SN_9A_2.fq.gz* UnKnow_1.fq.gz* UnKnow_2.fq.gz* bgi_project_summary.tar.gz* checksums.md5 index.lst md5.check* md5.txt* md51.txt readme.md split.sh
%%bash
mkdir /data/20170306_fastqc_gbs
cd /data/20170306_fastqc_gbs/
/data/20170306_fastqc_gbs
%%bash
time for file in /owl_web/nightingales/O_lurida/20160223_gbs/1[HNS]*.gz
do
cp "$file" .
done
real 25m31.705s user 0m0.070s sys 4m9.310s
The code above uses looks for all gzipped files (.gz) that start with "1", followed by either a "H", "N", or "S".
ls -1 | wc -l
247
ARRRGGHH! My connection crashed during the copy command and I forgot that I needed to change to the working directory specified in Input 7 above... That explains why the ls -1 | wc -l has so many files. Going to move them over to my desired directory.
%%bash
time for file in /owl_web/nightingales/O_lurida/20160223_gbs/1[HNS]*.gz
do
mv "$file" /data/20170306_fastqc_gbs/
done
real 12m25.731s user 0m1.040s sys 4m9.830s
cd /data/20170306_fastqc_gbs/
/data/20170306_fastqc_gbs
ls -1 | wc -l
193
Hmmm, I was expecting 192 files (96 samples x 2 files per sample). Let's see what's going on.
ls -l
total 29095420 -rwxrwxrwx 1 srlab staff 154481135 Feb 19 2016 1HL_10A_1.fq.gz* -rwxrwxrwx 1 srlab staff 193383163 Feb 19 2016 1HL_10A_2.fq.gz* -rwxrwxrwx 1 srlab staff 172568431 Feb 19 2016 1HL_11A_1.fq.gz* -rwxrwxrwx 1 srlab staff 215945074 Feb 19 2016 1HL_11A_2.fq.gz* -rwxrwxrwx 1 srlab staff 121896571 Feb 19 2016 1HL_12A_1.fq.gz* -rwxrwxrwx 1 srlab staff 153769201 Feb 19 2016 1HL_12A_2.fq.gz* -rwxrwxrwx 1 srlab staff 129166835 Feb 19 2016 1HL_13A_1.fq.gz* -rwxrwxrwx 1 srlab staff 162561925 Feb 19 2016 1HL_13A_2.fq.gz* -rwxrwxrwx 1 srlab staff 96637858 Feb 19 2016 1HL_14A_1.fq.gz* -rwxrwxrwx 1 srlab staff 122495363 Feb 19 2016 1HL_14A_2.fq.gz* -rwxrwxrwx 1 srlab staff 105831812 Feb 19 2016 1HL_15A_1.fq.gz* -rwxrwxrwx 1 srlab staff 133975748 Feb 19 2016 1HL_15A_2.fq.gz* -rwxrwxrwx 1 srlab staff 111612361 Feb 19 2016 1HL_16A_1.fq.gz* -rwxrwxrwx 1 srlab staff 141902372 Feb 19 2016 1HL_16A_2.fq.gz* -rwxrwxrwx 1 srlab staff 174464590 Feb 19 2016 1HL_17A_1.fq.gz* -rwxrwxrwx 1 srlab staff 222106070 Feb 19 2016 1HL_17A_2.fq.gz* -rwxrwxrwx 1 srlab staff 173635826 Feb 19 2016 1HL_19A_1.fq.gz* -rwxrwxrwx 1 srlab staff 220222361 Feb 19 2016 1HL_19A_2.fq.gz* -rwxrwxrwx 1 srlab staff 109908297 Feb 19 2016 1HL_1A_1.fq.gz* -rwxrwxrwx 1 srlab staff 137678314 Feb 19 2016 1HL_1A_2.fq.gz* -rwxrwxrwx 1 srlab staff 138809710 Feb 19 2016 1HL_20A_1.fq.gz* -rwxrwxrwx 1 srlab staff 176264839 Feb 19 2016 1HL_20A_2.fq.gz* -rwxrwxrwx 1 srlab staff 124489098 Feb 19 2016 1HL_21A_1.fq.gz* -rwxrwxrwx 1 srlab staff 157592064 Feb 19 2016 1HL_21A_2.fq.gz* -rwxrwxrwx 1 srlab staff 100198417 Feb 19 2016 1HL_22A_1.fq.gz* -rwxrwxrwx 1 srlab staff 126892686 Feb 19 2016 1HL_22A_2.fq.gz* -rwxrwxrwx 1 srlab staff 173557923 Feb 19 2016 1HL_23A_1.fq.gz* -rwxrwxrwx 1 srlab staff 219069850 Feb 19 2016 1HL_23A_2.fq.gz* -rwxrwxrwx 1 srlab staff 129669251 Feb 19 2016 1HL_24A_1.fq.gz* -rwxrwxrwx 1 srlab staff 165399832 Feb 19 2016 1HL_24A_2.fq.gz* -rwxrwxrwx 1 srlab staff 141822226 Feb 19 2016 1HL_25A_1.fq.gz* -rwxrwxrwx 1 srlab staff 179902025 Feb 19 2016 1HL_25A_2.fq.gz* -rwxrwxrwx 1 srlab staff 150618762 Feb 19 2016 1HL_26A_1.fq.gz* -rwxrwxrwx 1 srlab staff 191375636 Feb 19 2016 1HL_26A_2.fq.gz* -rwxrwxrwx 1 srlab staff 153881598 Feb 19 2016 1HL_27A_1.fq.gz* -rwxrwxrwx 1 srlab staff 194586520 Feb 19 2016 1HL_27A_2.fq.gz* -rwxrwxrwx 1 srlab staff 181691175 Feb 19 2016 1HL_28A_1.fq.gz* -rwxrwxrwx 1 srlab staff 247057324 Feb 19 2016 1HL_28A_2.fq.gz* -rwxrwxrwx 1 srlab staff 146511674 Feb 19 2016 1HL_29A_1.fq.gz* -rwxrwxrwx 1 srlab staff 186863101 Feb 19 2016 1HL_29A_2.fq.gz* -rwxrwxrwx 1 srlab staff 133292793 Feb 19 2016 1HL_2A_1.fq.gz* -rwxrwxrwx 1 srlab staff 167131705 Feb 19 2016 1HL_2A_2.fq.gz* -rwxrwxrwx 1 srlab staff 116889528 Feb 19 2016 1HL_31A_1.fq.gz* -rwxrwxrwx 1 srlab staff 149120509 Feb 19 2016 1HL_31A_2.fq.gz* -rwxrwxrwx 1 srlab staff 129240848 Feb 19 2016 1HL_33A_1.fq.gz* -rwxrwxrwx 1 srlab staff 164787435 Feb 19 2016 1HL_33A_2.fq.gz* -rwxrwxrwx 1 srlab staff 138720230 Feb 19 2016 1HL_34A_1.fq.gz* -rwxrwxrwx 1 srlab staff 175786634 Feb 19 2016 1HL_34A_2.fq.gz* -rwxrwxrwx 1 srlab staff 125842325 Feb 19 2016 1HL_35A_1.fq.gz* -rwxrwxrwx 1 srlab staff 159937484 Feb 19 2016 1HL_35A_2.fq.gz* -rwxrwxrwx 1 srlab staff 107372200 Feb 19 2016 1HL_3A_1.fq.gz* -rwxrwxrwx 1 srlab staff 134079837 Feb 19 2016 1HL_3A_2.fq.gz* -rwxrwxrwx 1 srlab staff 124275563 Feb 19 2016 1HL_4A_1.fq.gz* -rwxrwxrwx 1 srlab staff 155577259 Feb 19 2016 1HL_4A_2.fq.gz* -rwxrwxrwx 1 srlab staff 96180209 Feb 19 2016 1HL_5A_1.fq.gz* -rwxrwxrwx 1 srlab staff 120075402 Feb 19 2016 1HL_5A_2.fq.gz* -rwxrwxrwx 1 srlab staff 100456180 Feb 19 2016 1HL_6A_1.fq.gz* -rwxrwxrwx 1 srlab staff 126950712 Feb 19 2016 1HL_6A_2.fq.gz* -rwxrwxrwx 1 srlab staff 135768339 Feb 19 2016 1HL_7A_1.fq.gz* -rwxrwxrwx 1 srlab staff 185534602 Feb 19 2016 1HL_7A_2.fq.gz* -rwxrwxrwx 1 srlab staff 123568877 Feb 19 2016 1HL_8A_1.fq.gz* -rwxrwxrwx 1 srlab staff 154243302 Feb 19 2016 1HL_8A_2.fq.gz* -rwxrwxrwx 1 srlab staff 137315233 Feb 19 2016 1HL_9A_1.fq.gz* -rwxrwxrwx 1 srlab staff 172380176 Feb 19 2016 1HL_9A_2.fq.gz* -rwxrwxrwx 1 srlab staff 106748719 Feb 19 2016 1NF_10A_1.fq.gz* -rwxrwxrwx 1 srlab staff 131490047 Feb 19 2016 1NF_10A_2.fq.gz* -rwxrwxrwx 1 srlab staff 112400872 Feb 19 2016 1NF_11A_1.fq.gz* -rwxrwxrwx 1 srlab staff 138156460 Feb 19 2016 1NF_11A_2.fq.gz* -rwxrwxrwx 1 srlab staff 108523380 Feb 19 2016 1NF_12A_1.fq.gz* -rwxrwxrwx 1 srlab staff 132639302 Feb 19 2016 1NF_12A_2.fq.gz* -rwxrwxrwx 1 srlab staff 191928543 Feb 19 2016 1NF_13A_1.fq.gz* -rwxrwxrwx 1 srlab staff 236039297 Feb 19 2016 1NF_13A_2.fq.gz* -rwxrwxrwx 1 srlab staff 134337644 Feb 19 2016 1NF_14A_1.fq.gz* -rwxrwxrwx 1 srlab staff 165748230 Feb 19 2016 1NF_14A_2.fq.gz* -rwxrwxrwx 1 srlab staff 126212308 Feb 19 2016 1NF_15A_1.fq.gz* -rwxrwxrwx 1 srlab staff 156013264 Feb 19 2016 1NF_15A_2.fq.gz* -rwxrwxrwx 1 srlab staff 132954656 Feb 19 2016 1NF_16A_1.fq.gz* -rwxrwxrwx 1 srlab staff 163716697 Feb 19 2016 1NF_16A_2.fq.gz* -rwxrwxrwx 1 srlab staff 154103811 Feb 19 2016 1NF_17A_1.fq.gz* -rwxrwxrwx 1 srlab staff 189674614 Feb 19 2016 1NF_17A_2.fq.gz* -rwxrwxrwx 1 srlab staff 86410295 Feb 19 2016 1NF_18A_1.fq.gz* -rwxrwxrwx 1 srlab staff 106618372 Feb 19 2016 1NF_18A_2.fq.gz* -rwxrwxrwx 1 srlab staff 100292030 Feb 19 2016 1NF_19A_1.fq.gz* -rwxrwxrwx 1 srlab staff 124664744 Feb 19 2016 1NF_19A_2.fq.gz* -rwxrwxrwx 1 srlab staff 67538375 Feb 19 2016 1NF_1A_1.fq.gz* -rwxrwxrwx 1 srlab staff 82826107 Feb 19 2016 1NF_1A_2.fq.gz* -rwxrwxrwx 1 srlab staff 121059955 Feb 19 2016 1NF_20A_1.fq.gz* -rwxrwxrwx 1 srlab staff 149355086 Feb 19 2016 1NF_20A_2.fq.gz* -rwxrwxrwx 1 srlab staff 151179112 Feb 19 2016 1NF_21A_1.fq.gz* -rwxrwxrwx 1 srlab staff 185357969 Feb 19 2016 1NF_21A_2.fq.gz* -rwxrwxrwx 1 srlab staff 142673512 Feb 19 2016 1NF_22A_1.fq.gz* -rwxrwxrwx 1 srlab staff 176328886 Feb 19 2016 1NF_22A_2.fq.gz* -rwxrwxrwx 1 srlab staff 158606242 Feb 19 2016 1NF_23A_1.fq.gz* -rwxrwxrwx 1 srlab staff 195491482 Feb 19 2016 1NF_23A_2.fq.gz* -rwxrwxrwx 1 srlab staff 149351471 Feb 19 2016 1NF_24A_1.fq.gz* -rwxrwxrwx 1 srlab staff 185153248 Feb 19 2016 1NF_24A_2.fq.gz* -rwxrwxrwx 1 srlab staff 108148253 Feb 19 2016 1NF_25A_1.fq.gz* -rwxrwxrwx 1 srlab staff 133873617 Feb 19 2016 1NF_25A_2.fq.gz* -rwxrwxrwx 1 srlab staff 145144498 Feb 19 2016 1NF_26A_1.fq.gz* -rwxrwxrwx 1 srlab staff 178248069 Feb 19 2016 1NF_26A_2.fq.gz* -rwxrwxrwx 1 srlab staff 112635901 Feb 19 2016 1NF_27A_1.fq.gz* -rwxrwxrwx 1 srlab staff 137697306 Feb 19 2016 1NF_27A_2.fq.gz* -rwxrwxrwx 1 srlab staff 116076528 Feb 19 2016 1NF_28A_1.fq.gz* -rwxrwxrwx 1 srlab staff 143248260 Feb 19 2016 1NF_28A_2.fq.gz* -rwxrwxrwx 1 srlab staff 187968488 Feb 19 2016 1NF_29A_1.fq.gz* -rwxrwxrwx 1 srlab staff 233270039 Feb 19 2016 1NF_29A_2.fq.gz* -rwxrwxrwx 1 srlab staff 172245304 Feb 19 2016 1NF_2A_1.fq.gz* -rwxrwxrwx 1 srlab staff 210134829 Feb 19 2016 1NF_2A_2.fq.gz* -rwxrwxrwx 1 srlab staff 133078918 Feb 19 2016 1NF_30A_1.fq.gz* -rwxrwxrwx 1 srlab staff 164424177 Feb 19 2016 1NF_30A_2.fq.gz* -rwxrwxrwx 1 srlab staff 175296089 Feb 19 2016 1NF_31A_1.fq.gz* -rwxrwxrwx 1 srlab staff 216617740 Feb 19 2016 1NF_31A_2.fq.gz* -rwxrwxrwx 1 srlab staff 172603868 Feb 19 2016 1NF_32A_1.fq.gz* -rwxrwxrwx 1 srlab staff 211154285 Feb 19 2016 1NF_32A_2.fq.gz* -rwxrwxrwx 1 srlab staff 128872361 Feb 19 2016 1NF_33A_1.fq.gz* -rwxrwxrwx 1 srlab staff 158153199 Feb 19 2016 1NF_33A_2.fq.gz* -rwxrwxrwx 1 srlab staff 179085256 Feb 19 2016 1NF_4A_1.fq.gz* -rwxrwxrwx 1 srlab staff 218324118 Feb 19 2016 1NF_4A_2.fq.gz* -rwxrwxrwx 1 srlab staff 138593097 Feb 19 2016 1NF_5A_1.fq.gz* -rwxrwxrwx 1 srlab staff 168698077 Feb 19 2016 1NF_5A_2.fq.gz* -rwxrwxrwx 1 srlab staff 120644474 Feb 19 2016 1NF_6A_1.fq.gz* -rwxrwxrwx 1 srlab staff 147519116 Feb 19 2016 1NF_6A_2.fq.gz* -rwxrwxrwx 1 srlab staff 128297291 Feb 19 2016 1NF_7A_1.fq.gz* -rwxrwxrwx 1 srlab staff 157004271 Feb 19 2016 1NF_7A_2.fq.gz* -rwxrwxrwx 1 srlab staff 138023437 Feb 19 2016 1NF_8A_1.fq.gz* -rwxrwxrwx 1 srlab staff 169766027 Feb 19 2016 1NF_8A_2.fq.gz* -rwxrwxrwx 1 srlab staff 168199545 Feb 19 2016 1NF_9A_1.fq.gz* -rwxrwxrwx 1 srlab staff 205642861 Feb 19 2016 1NF_9A_2.fq.gz* -rwxrwxrwx 1 srlab staff 125332644 Feb 19 2016 1SN_10A_1.fq.gz* -rwxrwxrwx 1 srlab staff 155571530 Feb 19 2016 1SN_10A_2.fq.gz* -rwxrwxrwx 1 srlab staff 125736776 Feb 19 2016 1SN_11A_1.fq.gz* -rwxrwxrwx 1 srlab staff 156849493 Feb 19 2016 1SN_11A_2.fq.gz* -rwxrwxrwx 1 srlab staff 167820675 Feb 19 2016 1SN_12A_1.fq.gz* -rwxrwxrwx 1 srlab staff 208342825 Feb 19 2016 1SN_12A_2.fq.gz* -rwxrwxrwx 1 srlab staff 144576690 Feb 19 2016 1SN_13A_1.fq.gz* -rwxrwxrwx 1 srlab staff 179351703 Feb 19 2016 1SN_13A_2.fq.gz* -rwxrwxrwx 1 srlab staff 173406822 Feb 19 2016 1SN_14A_1.fq.gz* -rwxrwxrwx 1 srlab staff 214930308 Feb 19 2016 1SN_14A_2.fq.gz* -rwxrwxrwx 1 srlab staff 122960936 Feb 19 2016 1SN_15A_1.fq.gz* -rwxrwxrwx 1 srlab staff 151995286 Feb 19 2016 1SN_15A_2.fq.gz* -rwxrwxrwx 1 srlab staff 128198075 Feb 19 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1SN_2A_2.fq.gz* -rwxrwxrwx 1 srlab staff 186281833 Feb 19 2016 1SN_30A_1.fq.gz* -rwxrwxrwx 1 srlab staff 233632225 Feb 19 2016 1SN_30A_2.fq.gz* -rwxrwxrwx 1 srlab staff 161805373 Feb 19 2016 1SN_31A_1.fq.gz* -rwxrwxrwx 1 srlab staff 202824217 Feb 19 2016 1SN_31A_2.fq.gz* -rwxrwxrwx 1 srlab staff 124098512 Feb 19 2016 1SN_32A_1.fq.gz* -rwxrwxrwx 1 srlab staff 155401613 Feb 19 2016 1SN_32A_2.fq.gz* -rwxrwxrwx 1 srlab staff 119964192 Feb 19 2016 1SN_3A_1.fq.gz* -rwxrwxrwx 1 srlab staff 149529631 Feb 19 2016 1SN_3A_2.fq.gz* -rwxrwxrwx 1 srlab staff 161238629 Feb 19 2016 1SN_4A_1.fq.gz* -rwxrwxrwx 1 srlab staff 199759065 Feb 19 2016 1SN_4A_2.fq.gz* -rwxrwxrwx 1 srlab staff 146635817 Feb 19 2016 1SN_5A_1.fq.gz* -rwxrwxrwx 1 srlab staff 182366599 Feb 19 2016 1SN_5A_2.fq.gz* -rwxrwxrwx 1 srlab staff 163886792 Feb 19 2016 1SN_6A_1.fq.gz* -rwxrwxrwx 1 srlab staff 204116155 Feb 19 2016 1SN_6A_2.fq.gz* -rwxrwxrwx 1 srlab staff 145178840 Feb 19 2016 1SN_7A_1.fq.gz* -rwxrwxrwx 1 srlab staff 180617295 Feb 19 2016 1SN_7A_2.fq.gz* -rwxrwxrwx 1 srlab staff 160562082 Feb 19 2016 1SN_8A_1.fq.gz* -rwxrwxrwx 1 srlab staff 198417784 Feb 19 2016 1SN_8A_2.fq.gz* -rwxrwxrwx 1 srlab staff 155816621 Feb 19 2016 1SN_9A_1.fq.gz* -rwxrwxrwx 1 srlab staff 192919423 Feb 19 2016 1SN_9A_2.fq.gz* -rw-r--r-- 1 srlab staff 9548 Mar 6 17:26 temp_checksums.md5
Ahhhh! That temp_checksums.md5 file must've been created before my computer crashed (I had started a series of cells to just process all the steps I wanted and the MD5 creation was one of them). Let's see if that command actually completed.
wc -l temp_checksums.md5
File "<ipython-input-7-8127ea4a70ba>", line 1 wc -l temp_checksums.md5 ^ SyntaxError: invalid syntax
%%bash
wc -l temp_checksums.md5
192 temp_checksums.md5
%%bash
head temp_checksums.md5
tail temp_checksums.md5
57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz 3d87907131c5bcca146a2e1eb82ceb92 1HL_10A_2.fq.gz bd666574d447d79b2607bfa182aeb754 1HL_11A_1.fq.gz 8053d67c5575b040708510ddc02c5123 1HL_11A_2.fq.gz 719547253c42a1c3690015014bda0f89 1HL_12A_1.fq.gz 6f837d3464573b30df9e7f67867491ae 1HL_12A_2.fq.gz 8772f45a2bcf1f7aa6669e027f25bcd5 1HL_13A_1.fq.gz 8914728623f52930aa88b15cece20d08 1HL_13A_2.fq.gz 91acc4b1d196b739be2bde44b14436c9 1HL_14A_1.fq.gz 0c7b91215e2ee08dabde2fa5ce311b34 1HL_14A_2.fq.gz be7c9d91bf5895b489a09989fe0c3d55 1SN_5A_1.fq.gz 02bd1ff849c4edf635c866e41f4ac158 1SN_5A_2.fq.gz eeeb78e7d9f73ab67bb4c5325ceb29d0 1SN_6A_1.fq.gz 28a761d01540930600fd4cb412367e65 1SN_6A_2.fq.gz ea6036ddc236793fddc9ee4c12615b70 1SN_7A_1.fq.gz 21a1b9bebedecf9043d1529d48ba461f 1SN_7A_2.fq.gz d29170e28d64b4dea984b31ff933c482 1SN_8A_1.fq.gz 94a786839caa3498da6e7cbd4b27496c 1SN_8A_2.fq.gz 659e9e5cce523f14de81da86daf4c38c 1SN_9A_1.fq.gz 5d77c5fd542657141e39e83d632948b6 1SN_9A_2.fq.gz
This command already ran, so I'm just posting the code I used to generate the checksums for posterity:
%%bash
time for file in *.gz
do
md5sum "$file" >> temp_checksums.md5
done
The checksums look complete, so I'll go ahead and compare them with the original checksums on Owl.
%%bash
head /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5
MD5 (1HL_10A_1.fq.gz) = 57875c749f21bed3d4e6619ef53596b7 MD5 (1HL_10A_2.fq.gz) = 3d87907131c5bcca146a2e1eb82ceb92 MD5 (1HL_11A_1.fq.gz) = bd666574d447d79b2607bfa182aeb754 MD5 (1HL_11A_2.fq.gz) = 8053d67c5575b040708510ddc02c5123 MD5 (1HL_12A_1.fq.gz) = 719547253c42a1c3690015014bda0f89 MD5 (1HL_12A_2.fq.gz) = 6f837d3464573b30df9e7f67867491ae MD5 (1HL_13A_1.fq.gz) = 8772f45a2bcf1f7aa6669e027f25bcd5 MD5 (1HL_13A_2.fq.gz) = 8914728623f52930aa88b15cece20d08 MD5 (1HL_14A_1.fq.gz) = 91acc4b1d196b739be2bde44b14436c9 MD5 (1HL_14A_2.fq.gz) = 0c7b91215e2ee08dabde2fa5ce311b34
Let's write these values to a temp file in our current directory (/data/20170306_fastqc_gbs) for ease of comparison. Will have to tweak the formatting to match, too...
First, let's try to pull out a desired record from the target file using grep and the -e (for regular expression pattern matching).
grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5
File "<ipython-input-11-d801eca7ac91>", line 1 grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 ^ SyntaxError: invalid syntax
%%bash
grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5
MD5 (1HL_10A_1.fq.gz) = 57875c749f21bed3d4e6619ef53596b7
Test out some formatting options...
The command below will use the grep from above to pull the desired record.
It pipes the result from grep to the translate (tr) command.
The tr command uses the -d (delete) argument to delete anything indicated in the single quotes that follow.
The result from that is then piped to awk.
awk prints the fourth field ($4 i.e. column), followed by the contents of the second field ($2).
%%bash
grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 $2}'
57875c749f21bed3d4e6619ef53596b71HL_10A_1.fq.gz
OK, I didn't specify a field separator for the output, so the content of the two columns is adjacent instead of separated by some whitespace. The whitespace is actually two consecutive spaces, so I've added this to the awk print statement: " "
%%bash
grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 " " $2}'
57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz
OK, that looks good. Will write to temp file for use in MD5 checksum comparison.
%%bash
grep -e 1[HNS]*.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 " " $2}' > owl_checksums.md5
Process is interrupted.
I killed the above command because I didn't format the grep command properly.
%%bash
grep "1[HNS]*.fq.gz" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 " " $2}' > owl_checksums.md5
%%bash
wc -l owl_checksums.md5
head owl_checksums.md5
tail owl_checksums.md5
98 owl_checksums.md5 57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz bd666574d447d79b2607bfa182aeb754 1HL_11A_1.fq.gz 719547253c42a1c3690015014bda0f89 1HL_12A_1.fq.gz 8772f45a2bcf1f7aa6669e027f25bcd5 1HL_13A_1.fq.gz 91acc4b1d196b739be2bde44b14436c9 1HL_14A_1.fq.gz e532bf27cd835ddc888b25fab8e12d58 1HL_15A_1.fq.gz bc7c5ba1c87cb972c087b545db29d378 1HL_16A_1.fq.gz 1e06f736f4d19fe6d09e903243284eda 1HL_17A_1.fq.gz 5051f00e153277d732e83e2742b1e2f6 1HL_19A_1.fq.gz 5bf8732899249f7ce103bf4f5c182180 1HL_1A_1.fq.gz 89fee054c43e95cc4f368f4bde3359bf 1SN_32A_1.fq.gz ba0ad341e401cf3c08db713fc2ccf95b 1SN_3A_1.fq.gz 52405bdd6e3aaa34966bb3edf202f994 1SN_4A_1.fq.gz be7c9d91bf5895b489a09989fe0c3d55 1SN_5A_1.fq.gz eeeb78e7d9f73ab67bb4c5325ceb29d0 1SN_6A_1.fq.gz ea6036ddc236793fddc9ee4c12615b70 1SN_7A_1.fq.gz d29170e28d64b4dea984b31ff933c482 1SN_8A_1.fq.gz 659e9e5cce523f14de81da86daf4c38c 1SN_9A_1.fq.gz 5b3d8d5ea6b82b6c27d87c8813e87c6d UnKnow_1.fq.gz afd18614b9f5694af1a59672821cd0db /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Ah! Two, too many! I realize this is because the some of the checksum values match the grep pattern!! Let's re-run it with some changes to the grep pattern...
%%bash
grep "1[HNS][FLN]*.fq.gz" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 " " $2}' > owl_checksums.md5
%%bash
wc -l owl_checksums.md5
head owl_checksums.md5
tail owl_checksums.md5
0 owl_checksums.md5
Hmmm, that's odd. Do I have to escape the periods in the filenames?
%%bash
grep "1[HNS][FLN]_*\.fq\.gz" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 " " $2}' > owl_checksums.md5
%%bash
wc -l owl_checksums.md5
head owl_checksums.md5
tail owl_checksums.md5
0 owl_checksums.md5
I think the asterisk is causing issues (possibly because it's interpreted as regex asterisk (match preceding character), instead of as shell globbing (expand asterisk to match all characters).
%%bash
grep "1[HNS][FLN]" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \
tr -d '()' | \
awk '{ print $4 " " $2}' > owl_checksums.md5
%%bash
wc -l owl_checksums.md5
head owl_checksums.md5
tail owl_checksums.md5
192 owl_checksums.md5 57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz 3d87907131c5bcca146a2e1eb82ceb92 1HL_10A_2.fq.gz bd666574d447d79b2607bfa182aeb754 1HL_11A_1.fq.gz 8053d67c5575b040708510ddc02c5123 1HL_11A_2.fq.gz 719547253c42a1c3690015014bda0f89 1HL_12A_1.fq.gz 6f837d3464573b30df9e7f67867491ae 1HL_12A_2.fq.gz 8772f45a2bcf1f7aa6669e027f25bcd5 1HL_13A_1.fq.gz 8914728623f52930aa88b15cece20d08 1HL_13A_2.fq.gz 91acc4b1d196b739be2bde44b14436c9 1HL_14A_1.fq.gz 0c7b91215e2ee08dabde2fa5ce311b34 1HL_14A_2.fq.gz be7c9d91bf5895b489a09989fe0c3d55 1SN_5A_1.fq.gz 02bd1ff849c4edf635c866e41f4ac158 1SN_5A_2.fq.gz eeeb78e7d9f73ab67bb4c5325ceb29d0 1SN_6A_1.fq.gz 28a761d01540930600fd4cb412367e65 1SN_6A_2.fq.gz ea6036ddc236793fddc9ee4c12615b70 1SN_7A_1.fq.gz 21a1b9bebedecf9043d1529d48ba461f 1SN_7A_2.fq.gz d29170e28d64b4dea984b31ff933c482 1SN_8A_1.fq.gz 94a786839caa3498da6e7cbd4b27496c 1SN_8A_2.fq.gz 659e9e5cce523f14de81da86daf4c38c 1SN_9A_1.fq.gz 5d77c5fd542657141e39e83d632948b6 1SN_9A_2.fq.gz
Success! Let's compare the two checksum files.
%%bash
diff owl_checksums.md5 temp_checksums.md5
echo $?
0
Beauty! No differences! Now that we're confident the files copied over without issue, we can run FastQC.
%%bash
which fastqc
/usr/local/bioinformatics/FastQC/fastqc
In order to take advantage of the --threads option (allows you to specify how much memory to assign to each input file; 250MB is allocated to each file), I need to have an option to list all of the FASTQ files. Going to try to store the list of FASTQ files in a shell variable. Have to remove the newlines (the \n in the code below) so the list of files is printed horizontally (i.e. separated by a space instead of a newline).
%%bash
FASTQ_LIST="$(ls -1 *.gz| tr '\n' ' ')"
%%bash
head $FASTQ_LIST
%%bash
echo "$FASTQ_LIST" | head
The three cells above show me that the bash variable is not available outside of its individual cell. Let's check it when all the commands are in a single cell.
%%bash
FASTQ_LIST="$(ls -1 *.gz| tr '\n' ' ')"
echo "$FASTQ_LIST" | head
1HL_10A_1.fq.gz 1HL_10A_2.fq.gz 1HL_11A_1.fq.gz 1HL_11A_2.fq.gz 1HL_12A_1.fq.gz 1HL_12A_2.fq.gz 1HL_13A_1.fq.gz 1HL_13A_2.fq.gz 1HL_14A_1.fq.gz 1HL_14A_2.fq.gz 1HL_15A_1.fq.gz 1HL_15A_2.fq.gz 1HL_16A_1.fq.gz 1HL_16A_2.fq.gz 1HL_17A_1.fq.gz 1HL_17A_2.fq.gz 1HL_19A_1.fq.gz 1HL_19A_2.fq.gz 1HL_1A_1.fq.gz 1HL_1A_2.fq.gz 1HL_20A_1.fq.gz 1HL_20A_2.fq.gz 1HL_21A_1.fq.gz 1HL_21A_2.fq.gz 1HL_22A_1.fq.gz 1HL_22A_2.fq.gz 1HL_23A_1.fq.gz 1HL_23A_2.fq.gz 1HL_24A_1.fq.gz 1HL_24A_2.fq.gz 1HL_25A_1.fq.gz 1HL_25A_2.fq.gz 1HL_26A_1.fq.gz 1HL_26A_2.fq.gz 1HL_27A_1.fq.gz 1HL_27A_2.fq.gz 1HL_28A_1.fq.gz 1HL_28A_2.fq.gz 1HL_29A_1.fq.gz 1HL_29A_2.fq.gz 1HL_2A_1.fq.gz 1HL_2A_2.fq.gz 1HL_31A_1.fq.gz 1HL_31A_2.fq.gz 1HL_33A_1.fq.gz 1HL_33A_2.fq.gz 1HL_34A_1.fq.gz 1HL_34A_2.fq.gz 1HL_35A_1.fq.gz 1HL_35A_2.fq.gz 1HL_3A_1.fq.gz 1HL_3A_2.fq.gz 1HL_4A_1.fq.gz 1HL_4A_2.fq.gz 1HL_5A_1.fq.gz 1HL_5A_2.fq.gz 1HL_6A_1.fq.gz 1HL_6A_2.fq.gz 1HL_7A_1.fq.gz 1HL_7A_2.fq.gz 1HL_8A_1.fq.gz 1HL_8A_2.fq.gz 1HL_9A_1.fq.gz 1HL_9A_2.fq.gz 1NF_10A_1.fq.gz 1NF_10A_2.fq.gz 1NF_11A_1.fq.gz 1NF_11A_2.fq.gz 1NF_12A_1.fq.gz 1NF_12A_2.fq.gz 1NF_13A_1.fq.gz 1NF_13A_2.fq.gz 1NF_14A_1.fq.gz 1NF_14A_2.fq.gz 1NF_15A_1.fq.gz 1NF_15A_2.fq.gz 1NF_16A_1.fq.gz 1NF_16A_2.fq.gz 1NF_17A_1.fq.gz 1NF_17A_2.fq.gz 1NF_18A_1.fq.gz 1NF_18A_2.fq.gz 1NF_19A_1.fq.gz 1NF_19A_2.fq.gz 1NF_1A_1.fq.gz 1NF_1A_2.fq.gz 1NF_20A_1.fq.gz 1NF_20A_2.fq.gz 1NF_21A_1.fq.gz 1NF_21A_2.fq.gz 1NF_22A_1.fq.gz 1NF_22A_2.fq.gz 1NF_23A_1.fq.gz 1NF_23A_2.fq.gz 1NF_24A_1.fq.gz 1NF_24A_2.fq.gz 1NF_25A_1.fq.gz 1NF_25A_2.fq.gz 1NF_26A_1.fq.gz 1NF_26A_2.fq.gz 1NF_27A_1.fq.gz 1NF_27A_2.fq.gz 1NF_28A_1.fq.gz 1NF_28A_2.fq.gz 1NF_29A_1.fq.gz 1NF_29A_2.fq.gz 1NF_2A_1.fq.gz 1NF_2A_2.fq.gz 1NF_30A_1.fq.gz 1NF_30A_2.fq.gz 1NF_31A_1.fq.gz 1NF_31A_2.fq.gz 1NF_32A_1.fq.gz 1NF_32A_2.fq.gz 1NF_33A_1.fq.gz 1NF_33A_2.fq.gz 1NF_4A_1.fq.gz 1NF_4A_2.fq.gz 1NF_5A_1.fq.gz 1NF_5A_2.fq.gz 1NF_6A_1.fq.gz 1NF_6A_2.fq.gz 1NF_7A_1.fq.gz 1NF_7A_2.fq.gz 1NF_8A_1.fq.gz 1NF_8A_2.fq.gz 1NF_9A_1.fq.gz 1NF_9A_2.fq.gz 1SN_10A_1.fq.gz 1SN_10A_2.fq.gz 1SN_11A_1.fq.gz 1SN_11A_2.fq.gz 1SN_12A_1.fq.gz 1SN_12A_2.fq.gz 1SN_13A_1.fq.gz 1SN_13A_2.fq.gz 1SN_14A_1.fq.gz 1SN_14A_2.fq.gz 1SN_15A_1.fq.gz 1SN_15A_2.fq.gz 1SN_16A_1.fq.gz 1SN_16A_2.fq.gz 1SN_17A_1.fq.gz 1SN_17A_2.fq.gz 1SN_18A_1.fq.gz 1SN_18A_2.fq.gz 1SN_19A_1.fq.gz 1SN_19A_2.fq.gz 1SN_1A_1.fq.gz 1SN_1A_2.fq.gz 1SN_20A_1.fq.gz 1SN_20A_2.fq.gz 1SN_21A_1.fq.gz 1SN_21A_2.fq.gz 1SN_22A_1.fq.gz 1SN_22A_2.fq.gz 1SN_23A_1.fq.gz 1SN_23A_2.fq.gz 1SN_24A_1.fq.gz 1SN_24A_2.fq.gz 1SN_25A_1.fq.gz 1SN_25A_2.fq.gz 1SN_26A_1.fq.gz 1SN_26A_2.fq.gz 1SN_27A_1.fq.gz 1SN_27A_2.fq.gz 1SN_28A_1.fq.gz 1SN_28A_2.fq.gz 1SN_29A_1.fq.gz 1SN_29A_2.fq.gz 1SN_2A_1.fq.gz 1SN_2A_2.fq.gz 1SN_30A_1.fq.gz 1SN_30A_2.fq.gz 1SN_31A_1.fq.gz 1SN_31A_2.fq.gz 1SN_32A_1.fq.gz 1SN_32A_2.fq.gz 1SN_3A_1.fq.gz 1SN_3A_2.fq.gz 1SN_4A_1.fq.gz 1SN_4A_2.fq.gz 1SN_5A_1.fq.gz 1SN_5A_2.fq.gz 1SN_6A_1.fq.gz 1SN_6A_2.fq.gz 1SN_7A_1.fq.gz 1SN_7A_2.fq.gz 1SN_8A_1.fq.gz 1SN_8A_2.fq.gz 1SN_9A_1.fq.gz 1SN_9A_2.fq.gz
Yep, that works. Let's run the FastQC command.
I'm using the following options:
--extract: Doesn't compress the ouput folder.
--threads 96: Use 96 threads to process files (250MB of memory is allocated to each file)
--quiet: Suppresses the stdout and only prints stderr.
%%bash
FASTQ_LIST="$(ls -1 *.gz| tr '\n' ' ')"
time fastqc --extract --threads 96 --quiet "$FASTQ_LIST"
Skipping '1HL_10A_1.fq.gz 1HL_10A_2.fq.gz 1HL_11A_1.fq.gz 1HL_11A_2.fq.gz 1HL_12A_1.fq.gz 1HL_12A_2.fq.gz 1HL_13A_1.fq.gz 1HL_13A_2.fq.gz 1HL_14A_1.fq.gz 1HL_14A_2.fq.gz 1HL_15A_1.fq.gz 1HL_15A_2.fq.gz 1HL_16A_1.fq.gz 1HL_16A_2.fq.gz 1HL_17A_1.fq.gz 1HL_17A_2.fq.gz 1HL_19A_1.fq.gz 1HL_19A_2.fq.gz 1HL_1A_1.fq.gz 1HL_1A_2.fq.gz 1HL_20A_1.fq.gz 1HL_20A_2.fq.gz 1HL_21A_1.fq.gz 1HL_21A_2.fq.gz 1HL_22A_1.fq.gz 1HL_22A_2.fq.gz 1HL_23A_1.fq.gz 1HL_23A_2.fq.gz 1HL_24A_1.fq.gz 1HL_24A_2.fq.gz 1HL_25A_1.fq.gz 1HL_25A_2.fq.gz 1HL_26A_1.fq.gz 1HL_26A_2.fq.gz 1HL_27A_1.fq.gz 1HL_27A_2.fq.gz 1HL_28A_1.fq.gz 1HL_28A_2.fq.gz 1HL_29A_1.fq.gz 1HL_29A_2.fq.gz 1HL_2A_1.fq.gz 1HL_2A_2.fq.gz 1HL_31A_1.fq.gz 1HL_31A_2.fq.gz 1HL_33A_1.fq.gz 1HL_33A_2.fq.gz 1HL_34A_1.fq.gz 1HL_34A_2.fq.gz 1HL_35A_1.fq.gz 1HL_35A_2.fq.gz 1HL_3A_1.fq.gz 1HL_3A_2.fq.gz 1HL_4A_1.fq.gz 1HL_4A_2.fq.gz 1HL_5A_1.fq.gz 1HL_5A_2.fq.gz 1HL_6A_1.fq.gz 1HL_6A_2.fq.gz 1HL_7A_1.fq.gz 1HL_7A_2.fq.gz 1HL_8A_1.fq.gz 1HL_8A_2.fq.gz 1HL_9A_1.fq.gz 1HL_9A_2.fq.gz 1NF_10A_1.fq.gz 1NF_10A_2.fq.gz 1NF_11A_1.fq.gz 1NF_11A_2.fq.gz 1NF_12A_1.fq.gz 1NF_12A_2.fq.gz 1NF_13A_1.fq.gz 1NF_13A_2.fq.gz 1NF_14A_1.fq.gz 1NF_14A_2.fq.gz 1NF_15A_1.fq.gz 1NF_15A_2.fq.gz 1NF_16A_1.fq.gz 1NF_16A_2.fq.gz 1NF_17A_1.fq.gz 1NF_17A_2.fq.gz 1NF_18A_1.fq.gz 1NF_18A_2.fq.gz 1NF_19A_1.fq.gz 1NF_19A_2.fq.gz 1NF_1A_1.fq.gz 1NF_1A_2.fq.gz 1NF_20A_1.fq.gz 1NF_20A_2.fq.gz 1NF_21A_1.fq.gz 1NF_21A_2.fq.gz 1NF_22A_1.fq.gz 1NF_22A_2.fq.gz 1NF_23A_1.fq.gz 1NF_23A_2.fq.gz 1NF_24A_1.fq.gz 1NF_24A_2.fq.gz 1NF_25A_1.fq.gz 1NF_25A_2.fq.gz 1NF_26A_1.fq.gz 1NF_26A_2.fq.gz 1NF_27A_1.fq.gz 1NF_27A_2.fq.gz 1NF_28A_1.fq.gz 1NF_28A_2.fq.gz 1NF_29A_1.fq.gz 1NF_29A_2.fq.gz 1NF_2A_1.fq.gz 1NF_2A_2.fq.gz 1NF_30A_1.fq.gz 1NF_30A_2.fq.gz 1NF_31A_1.fq.gz 1NF_31A_2.fq.gz 1NF_32A_1.fq.gz 1NF_32A_2.fq.gz 1NF_33A_1.fq.gz 1NF_33A_2.fq.gz 1NF_4A_1.fq.gz 1NF_4A_2.fq.gz 1NF_5A_1.fq.gz 1NF_5A_2.fq.gz 1NF_6A_1.fq.gz 1NF_6A_2.fq.gz 1NF_7A_1.fq.gz 1NF_7A_2.fq.gz 1NF_8A_1.fq.gz 1NF_8A_2.fq.gz 1NF_9A_1.fq.gz 1NF_9A_2.fq.gz 1SN_10A_1.fq.gz 1SN_10A_2.fq.gz 1SN_11A_1.fq.gz 1SN_11A_2.fq.gz 1SN_12A_1.fq.gz 1SN_12A_2.fq.gz 1SN_13A_1.fq.gz 1SN_13A_2.fq.gz 1SN_14A_1.fq.gz 1SN_14A_2.fq.gz 1SN_15A_1.fq.gz 1SN_15A_2.fq.gz 1SN_16A_1.fq.gz 1SN_16A_2.fq.gz 1SN_17A_1.fq.gz 1SN_17A_2.fq.gz 1SN_18A_1.fq.gz 1SN_18A_2.fq.gz 1SN_19A_1.fq.gz 1SN_19A_2.fq.gz 1SN_1A_1.fq.gz 1SN_1A_2.fq.gz 1SN_20A_1.fq.gz 1SN_20A_2.fq.gz 1SN_21A_1.fq.gz 1SN_21A_2.fq.gz 1SN_22A_1.fq.gz 1SN_22A_2.fq.gz 1SN_23A_1.fq.gz 1SN_23A_2.fq.gz 1SN_24A_1.fq.gz 1SN_24A_2.fq.gz 1SN_25A_1.fq.gz 1SN_25A_2.fq.gz 1SN_26A_1.fq.gz 1SN_26A_2.fq.gz 1SN_27A_1.fq.gz 1SN_27A_2.fq.gz 1SN_28A_1.fq.gz 1SN_28A_2.fq.gz 1SN_29A_1.fq.gz 1SN_29A_2.fq.gz 1SN_2A_1.fq.gz 1SN_2A_2.fq.gz 1SN_30A_1.fq.gz 1SN_30A_2.fq.gz 1SN_31A_1.fq.gz 1SN_31A_2.fq.gz 1SN_32A_1.fq.gz 1SN_32A_2.fq.gz 1SN_3A_1.fq.gz 1SN_3A_2.fq.gz 1SN_4A_1.fq.gz 1SN_4A_2.fq.gz 1SN_5A_1.fq.gz 1SN_5A_2.fq.gz 1SN_6A_1.fq.gz 1SN_6A_2.fq.gz 1SN_7A_1.fq.gz 1SN_7A_2.fq.gz 1SN_8A_1.fq.gz 1SN_8A_2.fq.gz 1SN_9A_1.fq.gz 1SN_9A_2.fq.gz ' which didn't exist, or couldn't be read real 0m0.203s user 0m0.160s sys 0m0.010s
Ha! The habit of always surrounding shell variables with quotations (to prevent elements in the variable that might contain spaces from screwing up a command) actually backfired! I WANT the spaces to be interepreted, because FastQC accepts a space-delimited list of filenames as input! By encasing the shell variable in quotes, FastQC viewed the entire list of files as a single input file!!
%%bash
FASTQ_LIST="$(ls -1 *.gz| tr '\n' ' ')"
time fastqc --extract --threads 96 --quiet $FASTQ_LIST
real 327m47.227s user 206m46.190s sys 322m21.800s
Let's see what was made. We'll ignore the gzipped FASTQ files using the --ignore argument.
%%bash
ls --ignore="*.gz"
1HL_10A_1_fastqc 1HL_10A_1_fastqc.html 1HL_10A_1_fastqc.zip 1HL_10A_2_fastqc 1HL_10A_2_fastqc.html 1HL_10A_2_fastqc.zip 1HL_11A_1_fastqc 1HL_11A_1_fastqc.html 1HL_11A_1_fastqc.zip 1HL_11A_2_fastqc 1HL_11A_2_fastqc.html 1HL_11A_2_fastqc.zip 1HL_12A_1_fastqc 1HL_12A_1_fastqc.html 1HL_12A_1_fastqc.zip 1HL_12A_2_fastqc 1HL_12A_2_fastqc.html 1HL_12A_2_fastqc.zip 1HL_13A_1_fastqc 1HL_13A_1_fastqc.html 1HL_13A_1_fastqc.zip 1HL_13A_2_fastqc 1HL_13A_2_fastqc.html 1HL_13A_2_fastqc.zip 1HL_14A_1_fastqc 1HL_14A_1_fastqc.html 1HL_14A_1_fastqc.zip 1HL_14A_2_fastqc 1HL_14A_2_fastqc.html 1HL_14A_2_fastqc.zip 1HL_15A_1_fastqc 1HL_15A_1_fastqc.html 1HL_15A_1_fastqc.zip 1HL_15A_2_fastqc 1HL_15A_2_fastqc.html 1HL_15A_2_fastqc.zip 1HL_16A_1_fastqc 1HL_16A_1_fastqc.html 1HL_16A_1_fastqc.zip 1HL_16A_2_fastqc 1HL_16A_2_fastqc.html 1HL_16A_2_fastqc.zip 1HL_17A_1_fastqc 1HL_17A_1_fastqc.html 1HL_17A_1_fastqc.zip 1HL_17A_2_fastqc 1HL_17A_2_fastqc.html 1HL_17A_2_fastqc.zip 1HL_19A_1_fastqc 1HL_19A_1_fastqc.html 1HL_19A_1_fastqc.zip 1HL_19A_2_fastqc 1HL_19A_2_fastqc.html 1HL_19A_2_fastqc.zip 1HL_1A_1_fastqc 1HL_1A_1_fastqc.html 1HL_1A_1_fastqc.zip 1HL_1A_2_fastqc 1HL_1A_2_fastqc.html 1HL_1A_2_fastqc.zip 1HL_20A_1_fastqc 1HL_20A_1_fastqc.html 1HL_20A_1_fastqc.zip 1HL_20A_2_fastqc 1HL_20A_2_fastqc.html 1HL_20A_2_fastqc.zip 1HL_21A_1_fastqc 1HL_21A_1_fastqc.html 1HL_21A_1_fastqc.zip 1HL_21A_2_fastqc 1HL_21A_2_fastqc.html 1HL_21A_2_fastqc.zip 1HL_22A_1_fastqc 1HL_22A_1_fastqc.html 1HL_22A_1_fastqc.zip 1HL_22A_2_fastqc 1HL_22A_2_fastqc.html 1HL_22A_2_fastqc.zip 1HL_23A_1_fastqc 1HL_23A_1_fastqc.html 1HL_23A_1_fastqc.zip 1HL_23A_2_fastqc 1HL_23A_2_fastqc.html 1HL_23A_2_fastqc.zip 1HL_24A_1_fastqc 1HL_24A_1_fastqc.html 1HL_24A_1_fastqc.zip 1HL_24A_2_fastqc 1HL_24A_2_fastqc.html 1HL_24A_2_fastqc.zip 1HL_25A_1_fastqc 1HL_25A_1_fastqc.html 1HL_25A_1_fastqc.zip 1HL_25A_2_fastqc 1HL_25A_2_fastqc.html 1HL_25A_2_fastqc.zip 1HL_26A_1_fastqc 1HL_26A_1_fastqc.html 1HL_26A_1_fastqc.zip 1HL_26A_2_fastqc 1HL_26A_2_fastqc.html 1HL_26A_2_fastqc.zip 1HL_27A_1_fastqc 1HL_27A_1_fastqc.html 1HL_27A_1_fastqc.zip 1HL_27A_2_fastqc 1HL_27A_2_fastqc.html 1HL_27A_2_fastqc.zip 1HL_28A_1_fastqc 1HL_28A_1_fastqc.html 1HL_28A_1_fastqc.zip 1HL_28A_2_fastqc 1HL_28A_2_fastqc.html 1HL_28A_2_fastqc.zip 1HL_29A_1_fastqc 1HL_29A_1_fastqc.html 1HL_29A_1_fastqc.zip 1HL_29A_2_fastqc 1HL_29A_2_fastqc.html 1HL_29A_2_fastqc.zip 1HL_2A_1_fastqc 1HL_2A_1_fastqc.html 1HL_2A_1_fastqc.zip 1HL_2A_2_fastqc 1HL_2A_2_fastqc.html 1HL_2A_2_fastqc.zip 1HL_31A_1_fastqc 1HL_31A_1_fastqc.html 1HL_31A_1_fastqc.zip 1HL_31A_2_fastqc 1HL_31A_2_fastqc.html 1HL_31A_2_fastqc.zip 1HL_33A_1_fastqc 1HL_33A_1_fastqc.html 1HL_33A_1_fastqc.zip 1HL_33A_2_fastqc 1HL_33A_2_fastqc.html 1HL_33A_2_fastqc.zip 1HL_34A_1_fastqc 1HL_34A_1_fastqc.html 1HL_34A_1_fastqc.zip 1HL_34A_2_fastqc 1HL_34A_2_fastqc.html 1HL_34A_2_fastqc.zip 1HL_35A_1_fastqc 1HL_35A_1_fastqc.html 1HL_35A_1_fastqc.zip 1HL_35A_2_fastqc 1HL_35A_2_fastqc.html 1HL_35A_2_fastqc.zip 1HL_3A_1_fastqc 1HL_3A_1_fastqc.html 1HL_3A_1_fastqc.zip 1HL_3A_2_fastqc 1HL_3A_2_fastqc.html 1HL_3A_2_fastqc.zip 1HL_4A_1_fastqc 1HL_4A_1_fastqc.html 1HL_4A_1_fastqc.zip 1HL_4A_2_fastqc 1HL_4A_2_fastqc.html 1HL_4A_2_fastqc.zip 1HL_5A_1_fastqc 1HL_5A_1_fastqc.html 1HL_5A_1_fastqc.zip 1HL_5A_2_fastqc 1HL_5A_2_fastqc.html 1HL_5A_2_fastqc.zip 1HL_6A_1_fastqc 1HL_6A_1_fastqc.html 1HL_6A_1_fastqc.zip 1HL_6A_2_fastqc 1HL_6A_2_fastqc.html 1HL_6A_2_fastqc.zip 1HL_7A_1_fastqc 1HL_7A_1_fastqc.html 1HL_7A_1_fastqc.zip 1HL_7A_2_fastqc 1HL_7A_2_fastqc.html 1HL_7A_2_fastqc.zip 1HL_8A_1_fastqc 1HL_8A_1_fastqc.html 1HL_8A_1_fastqc.zip 1HL_8A_2_fastqc 1HL_8A_2_fastqc.html 1HL_8A_2_fastqc.zip 1HL_9A_1_fastqc 1HL_9A_1_fastqc.html 1HL_9A_1_fastqc.zip 1HL_9A_2_fastqc 1HL_9A_2_fastqc.html 1HL_9A_2_fastqc.zip 1NF_10A_1_fastqc 1NF_10A_1_fastqc.html 1NF_10A_1_fastqc.zip 1NF_10A_2_fastqc 1NF_10A_2_fastqc.html 1NF_10A_2_fastqc.zip 1NF_11A_1_fastqc 1NF_11A_1_fastqc.html 1NF_11A_1_fastqc.zip 1NF_11A_2_fastqc 1NF_11A_2_fastqc.html 1NF_11A_2_fastqc.zip 1NF_12A_1_fastqc 1NF_12A_1_fastqc.html 1NF_12A_1_fastqc.zip 1NF_12A_2_fastqc 1NF_12A_2_fastqc.html 1NF_12A_2_fastqc.zip 1NF_13A_1_fastqc 1NF_13A_1_fastqc.html 1NF_13A_1_fastqc.zip 1NF_13A_2_fastqc 1NF_13A_2_fastqc.html 1NF_13A_2_fastqc.zip 1NF_14A_1_fastqc 1NF_14A_1_fastqc.html 1NF_14A_1_fastqc.zip 1NF_14A_2_fastqc 1NF_14A_2_fastqc.html 1NF_14A_2_fastqc.zip 1NF_15A_1_fastqc 1NF_15A_1_fastqc.html 1NF_15A_1_fastqc.zip 1NF_15A_2_fastqc 1NF_15A_2_fastqc.html 1NF_15A_2_fastqc.zip 1NF_16A_1_fastqc 1NF_16A_1_fastqc.html 1NF_16A_1_fastqc.zip 1NF_16A_2_fastqc 1NF_16A_2_fastqc.html 1NF_16A_2_fastqc.zip 1NF_17A_1_fastqc 1NF_17A_1_fastqc.html 1NF_17A_1_fastqc.zip 1NF_17A_2_fastqc 1NF_17A_2_fastqc.html 1NF_17A_2_fastqc.zip 1NF_18A_1_fastqc 1NF_18A_1_fastqc.html 1NF_18A_1_fastqc.zip 1NF_18A_2_fastqc 1NF_18A_2_fastqc.html 1NF_18A_2_fastqc.zip 1NF_19A_1_fastqc 1NF_19A_1_fastqc.html 1NF_19A_1_fastqc.zip 1NF_19A_2_fastqc 1NF_19A_2_fastqc.html 1NF_19A_2_fastqc.zip 1NF_1A_1_fastqc 1NF_1A_1_fastqc.html 1NF_1A_1_fastqc.zip 1NF_1A_2_fastqc 1NF_1A_2_fastqc.html 1NF_1A_2_fastqc.zip 1NF_20A_1_fastqc 1NF_20A_1_fastqc.html 1NF_20A_1_fastqc.zip 1NF_20A_2_fastqc 1NF_20A_2_fastqc.html 1NF_20A_2_fastqc.zip 1NF_21A_1_fastqc 1NF_21A_1_fastqc.html 1NF_21A_1_fastqc.zip 1NF_21A_2_fastqc 1NF_21A_2_fastqc.html 1NF_21A_2_fastqc.zip 1NF_22A_1_fastqc 1NF_22A_1_fastqc.html 1NF_22A_1_fastqc.zip 1NF_22A_2_fastqc 1NF_22A_2_fastqc.html 1NF_22A_2_fastqc.zip 1NF_23A_1_fastqc 1NF_23A_1_fastqc.html 1NF_23A_1_fastqc.zip 1NF_23A_2_fastqc 1NF_23A_2_fastqc.html 1NF_23A_2_fastqc.zip 1NF_24A_1_fastqc 1NF_24A_1_fastqc.html 1NF_24A_1_fastqc.zip 1NF_24A_2_fastqc 1NF_24A_2_fastqc.html 1NF_24A_2_fastqc.zip 1NF_25A_1_fastqc 1NF_25A_1_fastqc.html 1NF_25A_1_fastqc.zip 1NF_25A_2_fastqc 1NF_25A_2_fastqc.html 1NF_25A_2_fastqc.zip 1NF_26A_1_fastqc 1NF_26A_1_fastqc.html 1NF_26A_1_fastqc.zip 1NF_26A_2_fastqc 1NF_26A_2_fastqc.html 1NF_26A_2_fastqc.zip 1NF_27A_1_fastqc 1NF_27A_1_fastqc.html 1NF_27A_1_fastqc.zip 1NF_27A_2_fastqc 1NF_27A_2_fastqc.html 1NF_27A_2_fastqc.zip 1NF_28A_1_fastqc 1NF_28A_1_fastqc.html 1NF_28A_1_fastqc.zip 1NF_28A_2_fastqc 1NF_28A_2_fastqc.html 1NF_28A_2_fastqc.zip 1NF_29A_1_fastqc 1NF_29A_1_fastqc.html 1NF_29A_1_fastqc.zip 1NF_29A_2_fastqc 1NF_29A_2_fastqc.html 1NF_29A_2_fastqc.zip 1NF_2A_1_fastqc 1NF_2A_1_fastqc.html 1NF_2A_1_fastqc.zip 1NF_2A_2_fastqc 1NF_2A_2_fastqc.html 1NF_2A_2_fastqc.zip 1NF_30A_1_fastqc 1NF_30A_1_fastqc.html 1NF_30A_1_fastqc.zip 1NF_30A_2_fastqc 1NF_30A_2_fastqc.html 1NF_30A_2_fastqc.zip 1NF_31A_1_fastqc 1NF_31A_1_fastqc.html 1NF_31A_1_fastqc.zip 1NF_31A_2_fastqc 1NF_31A_2_fastqc.html 1NF_31A_2_fastqc.zip 1NF_32A_1_fastqc 1NF_32A_1_fastqc.html 1NF_32A_1_fastqc.zip 1NF_32A_2_fastqc 1NF_32A_2_fastqc.html 1NF_32A_2_fastqc.zip 1NF_33A_1_fastqc 1NF_33A_1_fastqc.html 1NF_33A_1_fastqc.zip 1NF_33A_2_fastqc 1NF_33A_2_fastqc.html 1NF_33A_2_fastqc.zip 1NF_4A_1_fastqc 1NF_4A_1_fastqc.html 1NF_4A_1_fastqc.zip 1NF_4A_2_fastqc 1NF_4A_2_fastqc.html 1NF_4A_2_fastqc.zip 1NF_5A_1_fastqc 1NF_5A_1_fastqc.html 1NF_5A_1_fastqc.zip 1NF_5A_2_fastqc 1NF_5A_2_fastqc.html 1NF_5A_2_fastqc.zip 1NF_6A_1_fastqc 1NF_6A_1_fastqc.html 1NF_6A_1_fastqc.zip 1NF_6A_2_fastqc 1NF_6A_2_fastqc.html 1NF_6A_2_fastqc.zip 1NF_7A_1_fastqc 1NF_7A_1_fastqc.html 1NF_7A_1_fastqc.zip 1NF_7A_2_fastqc 1NF_7A_2_fastqc.html 1NF_7A_2_fastqc.zip 1NF_8A_1_fastqc 1NF_8A_1_fastqc.html 1NF_8A_1_fastqc.zip 1NF_8A_2_fastqc 1NF_8A_2_fastqc.html 1NF_8A_2_fastqc.zip 1NF_9A_1_fastqc 1NF_9A_1_fastqc.html 1NF_9A_1_fastqc.zip 1NF_9A_2_fastqc 1NF_9A_2_fastqc.html 1NF_9A_2_fastqc.zip 1SN_10A_1_fastqc 1SN_10A_1_fastqc.html 1SN_10A_1_fastqc.zip 1SN_10A_2_fastqc 1SN_10A_2_fastqc.html 1SN_10A_2_fastqc.zip 1SN_11A_1_fastqc 1SN_11A_1_fastqc.html 1SN_11A_1_fastqc.zip 1SN_11A_2_fastqc 1SN_11A_2_fastqc.html 1SN_11A_2_fastqc.zip 1SN_12A_1_fastqc 1SN_12A_1_fastqc.html 1SN_12A_1_fastqc.zip 1SN_12A_2_fastqc 1SN_12A_2_fastqc.html 1SN_12A_2_fastqc.zip 1SN_13A_1_fastqc 1SN_13A_1_fastqc.html 1SN_13A_1_fastqc.zip 1SN_13A_2_fastqc 1SN_13A_2_fastqc.html 1SN_13A_2_fastqc.zip 1SN_14A_1_fastqc 1SN_14A_1_fastqc.html 1SN_14A_1_fastqc.zip 1SN_14A_2_fastqc 1SN_14A_2_fastqc.html 1SN_14A_2_fastqc.zip 1SN_15A_1_fastqc 1SN_15A_1_fastqc.html 1SN_15A_1_fastqc.zip 1SN_15A_2_fastqc 1SN_15A_2_fastqc.html 1SN_15A_2_fastqc.zip 1SN_16A_1_fastqc 1SN_16A_1_fastqc.html 1SN_16A_1_fastqc.zip 1SN_16A_2_fastqc 1SN_16A_2_fastqc.html 1SN_16A_2_fastqc.zip 1SN_17A_1_fastqc 1SN_17A_1_fastqc.html 1SN_17A_1_fastqc.zip 1SN_17A_2_fastqc 1SN_17A_2_fastqc.html 1SN_17A_2_fastqc.zip 1SN_18A_1_fastqc 1SN_18A_1_fastqc.html 1SN_18A_1_fastqc.zip 1SN_18A_2_fastqc 1SN_18A_2_fastqc.html 1SN_18A_2_fastqc.zip 1SN_19A_1_fastqc 1SN_19A_1_fastqc.html 1SN_19A_1_fastqc.zip 1SN_19A_2_fastqc 1SN_19A_2_fastqc.html 1SN_19A_2_fastqc.zip 1SN_1A_1_fastqc 1SN_1A_1_fastqc.html 1SN_1A_1_fastqc.zip 1SN_1A_2_fastqc 1SN_1A_2_fastqc.html 1SN_1A_2_fastqc.zip 1SN_20A_1_fastqc 1SN_20A_1_fastqc.html 1SN_20A_1_fastqc.zip 1SN_20A_2_fastqc 1SN_20A_2_fastqc.html 1SN_20A_2_fastqc.zip 1SN_21A_1_fastqc 1SN_21A_1_fastqc.html 1SN_21A_1_fastqc.zip 1SN_21A_2_fastqc 1SN_21A_2_fastqc.html 1SN_21A_2_fastqc.zip 1SN_22A_1_fastqc 1SN_22A_1_fastqc.html 1SN_22A_1_fastqc.zip 1SN_22A_2_fastqc 1SN_22A_2_fastqc.html 1SN_22A_2_fastqc.zip 1SN_23A_1_fastqc 1SN_23A_1_fastqc.html 1SN_23A_1_fastqc.zip 1SN_23A_2_fastqc 1SN_23A_2_fastqc.html 1SN_23A_2_fastqc.zip 1SN_24A_1_fastqc 1SN_24A_1_fastqc.html 1SN_24A_1_fastqc.zip 1SN_24A_2_fastqc 1SN_24A_2_fastqc.html 1SN_24A_2_fastqc.zip 1SN_25A_1_fastqc 1SN_25A_1_fastqc.html 1SN_25A_1_fastqc.zip 1SN_25A_2_fastqc 1SN_25A_2_fastqc.html 1SN_25A_2_fastqc.zip 1SN_26A_1_fastqc 1SN_26A_1_fastqc.html 1SN_26A_1_fastqc.zip 1SN_26A_2_fastqc 1SN_26A_2_fastqc.html 1SN_26A_2_fastqc.zip 1SN_27A_1_fastqc 1SN_27A_1_fastqc.html 1SN_27A_1_fastqc.zip 1SN_27A_2_fastqc 1SN_27A_2_fastqc.html 1SN_27A_2_fastqc.zip 1SN_28A_1_fastqc 1SN_28A_1_fastqc.html 1SN_28A_1_fastqc.zip 1SN_28A_2_fastqc 1SN_28A_2_fastqc.html 1SN_28A_2_fastqc.zip 1SN_29A_1_fastqc 1SN_29A_1_fastqc.html 1SN_29A_1_fastqc.zip 1SN_29A_2_fastqc 1SN_29A_2_fastqc.html 1SN_29A_2_fastqc.zip 1SN_2A_1_fastqc 1SN_2A_1_fastqc.html 1SN_2A_1_fastqc.zip 1SN_2A_2_fastqc 1SN_2A_2_fastqc.html 1SN_2A_2_fastqc.zip 1SN_30A_1_fastqc 1SN_30A_1_fastqc.html 1SN_30A_1_fastqc.zip 1SN_30A_2_fastqc 1SN_30A_2_fastqc.html 1SN_30A_2_fastqc.zip 1SN_31A_1_fastqc 1SN_31A_1_fastqc.html 1SN_31A_1_fastqc.zip 1SN_31A_2_fastqc 1SN_31A_2_fastqc.html 1SN_31A_2_fastqc.zip 1SN_32A_1_fastqc 1SN_32A_1_fastqc.html 1SN_32A_1_fastqc.zip 1SN_32A_2_fastqc 1SN_32A_2_fastqc.html 1SN_32A_2_fastqc.zip 1SN_3A_1_fastqc 1SN_3A_1_fastqc.html 1SN_3A_1_fastqc.zip 1SN_3A_2_fastqc 1SN_3A_2_fastqc.html 1SN_3A_2_fastqc.zip 1SN_4A_1_fastqc 1SN_4A_1_fastqc.html 1SN_4A_1_fastqc.zip 1SN_4A_2_fastqc 1SN_4A_2_fastqc.html 1SN_4A_2_fastqc.zip 1SN_5A_1_fastqc 1SN_5A_1_fastqc.html 1SN_5A_1_fastqc.zip 1SN_5A_2_fastqc 1SN_5A_2_fastqc.html 1SN_5A_2_fastqc.zip 1SN_6A_1_fastqc 1SN_6A_1_fastqc.html 1SN_6A_1_fastqc.zip 1SN_6A_2_fastqc 1SN_6A_2_fastqc.html 1SN_6A_2_fastqc.zip 1SN_7A_1_fastqc 1SN_7A_1_fastqc.html 1SN_7A_1_fastqc.zip 1SN_7A_2_fastqc 1SN_7A_2_fastqc.html 1SN_7A_2_fastqc.zip 1SN_8A_1_fastqc 1SN_8A_1_fastqc.html 1SN_8A_1_fastqc.zip 1SN_8A_2_fastqc 1SN_8A_2_fastqc.html 1SN_8A_2_fastqc.zip 1SN_9A_1_fastqc 1SN_9A_1_fastqc.html 1SN_9A_1_fastqc.zip 1SN_9A_2_fastqc 1SN_9A_2_fastqc.html 1SN_9A_2_fastqc.zip outputtest.txt owl_checksums.md5 temp_checksums.md5
Cool, fastqc output! Let's look in one of the folders to see what's doin'.
ls 1SN_9A_1_fastqc/
Icons/ Images/ fastqc.fo fastqc_data.txt fastqc_report.html summary.txt
Let's make sure there's FastQC output for each input file (there should be 192 .zip files)
ls -1 *.zip | wc -l
192
Move FastQC output folders to Owl.
The -t specifies the target directory. I think this is needed so that each folder that is moved keeps the folder name, instead of just copying the contents within the folder to the destination...
%%bash
time \
mv \
-t /owl_web/nightingales/O_lurida/20160223_gbs/ \
*fastqc/
real 2m15.669s user 0m0.030s sys 0m13.490s
%%bash
ls --ignore="*.gz"
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1NF_12A_2_fastqc.zip 1NF_13A_1_fastqc.html 1NF_13A_1_fastqc.zip 1NF_13A_2_fastqc.html 1NF_13A_2_fastqc.zip 1NF_14A_1_fastqc.html 1NF_14A_1_fastqc.zip 1NF_14A_2_fastqc.html 1NF_14A_2_fastqc.zip 1NF_15A_1_fastqc.html 1NF_15A_1_fastqc.zip 1NF_15A_2_fastqc.html 1NF_15A_2_fastqc.zip 1NF_16A_1_fastqc.html 1NF_16A_1_fastqc.zip 1NF_16A_2_fastqc.html 1NF_16A_2_fastqc.zip 1NF_17A_1_fastqc.html 1NF_17A_1_fastqc.zip 1NF_17A_2_fastqc.html 1NF_17A_2_fastqc.zip 1NF_18A_1_fastqc.html 1NF_18A_1_fastqc.zip 1NF_18A_2_fastqc.html 1NF_18A_2_fastqc.zip 1NF_19A_1_fastqc.html 1NF_19A_1_fastqc.zip 1NF_19A_2_fastqc.html 1NF_19A_2_fastqc.zip 1NF_1A_1_fastqc.html 1NF_1A_1_fastqc.zip 1NF_1A_2_fastqc.html 1NF_1A_2_fastqc.zip 1NF_20A_1_fastqc.html 1NF_20A_1_fastqc.zip 1NF_20A_2_fastqc.html 1NF_20A_2_fastqc.zip 1NF_21A_1_fastqc.html 1NF_21A_1_fastqc.zip 1NF_21A_2_fastqc.html 1NF_21A_2_fastqc.zip 1NF_22A_1_fastqc.html 1NF_22A_1_fastqc.zip 1NF_22A_2_fastqc.html 1NF_22A_2_fastqc.zip 1NF_23A_1_fastqc.html 1NF_23A_1_fastqc.zip 1NF_23A_2_fastqc.html 1NF_23A_2_fastqc.zip 1NF_24A_1_fastqc.html 1NF_24A_1_fastqc.zip 1NF_24A_2_fastqc.html 1NF_24A_2_fastqc.zip 1NF_25A_1_fastqc.html 1NF_25A_1_fastqc.zip 1NF_25A_2_fastqc.html 1NF_25A_2_fastqc.zip 1NF_26A_1_fastqc.html 1NF_26A_1_fastqc.zip 1NF_26A_2_fastqc.html 1NF_26A_2_fastqc.zip 1NF_27A_1_fastqc.html 1NF_27A_1_fastqc.zip 1NF_27A_2_fastqc.html 1NF_27A_2_fastqc.zip 1NF_28A_1_fastqc.html 1NF_28A_1_fastqc.zip 1NF_28A_2_fastqc.html 1NF_28A_2_fastqc.zip 1NF_29A_1_fastqc.html 1NF_29A_1_fastqc.zip 1NF_29A_2_fastqc.html 1NF_29A_2_fastqc.zip 1NF_2A_1_fastqc.html 1NF_2A_1_fastqc.zip 1NF_2A_2_fastqc.html 1NF_2A_2_fastqc.zip 1NF_30A_1_fastqc.html 1NF_30A_1_fastqc.zip 1NF_30A_2_fastqc.html 1NF_30A_2_fastqc.zip 1NF_31A_1_fastqc.html 1NF_31A_1_fastqc.zip 1NF_31A_2_fastqc.html 1NF_31A_2_fastqc.zip 1NF_32A_1_fastqc.html 1NF_32A_1_fastqc.zip 1NF_32A_2_fastqc.html 1NF_32A_2_fastqc.zip 1NF_33A_1_fastqc.html 1NF_33A_1_fastqc.zip 1NF_33A_2_fastqc.html 1NF_33A_2_fastqc.zip 1NF_4A_1_fastqc.html 1NF_4A_1_fastqc.zip 1NF_4A_2_fastqc.html 1NF_4A_2_fastqc.zip 1NF_5A_1_fastqc.html 1NF_5A_1_fastqc.zip 1NF_5A_2_fastqc.html 1NF_5A_2_fastqc.zip 1NF_6A_1_fastqc.html 1NF_6A_1_fastqc.zip 1NF_6A_2_fastqc.html 1NF_6A_2_fastqc.zip 1NF_7A_1_fastqc.html 1NF_7A_1_fastqc.zip 1NF_7A_2_fastqc.html 1NF_7A_2_fastqc.zip 1NF_8A_1_fastqc.html 1NF_8A_1_fastqc.zip 1NF_8A_2_fastqc.html 1NF_8A_2_fastqc.zip 1NF_9A_1_fastqc.html 1NF_9A_1_fastqc.zip 1NF_9A_2_fastqc.html 1NF_9A_2_fastqc.zip 1SN_10A_1_fastqc.html 1SN_10A_1_fastqc.zip 1SN_10A_2_fastqc.html 1SN_10A_2_fastqc.zip 1SN_11A_1_fastqc.html 1SN_11A_1_fastqc.zip 1SN_11A_2_fastqc.html 1SN_11A_2_fastqc.zip 1SN_12A_1_fastqc.html 1SN_12A_1_fastqc.zip 1SN_12A_2_fastqc.html 1SN_12A_2_fastqc.zip 1SN_13A_1_fastqc.html 1SN_13A_1_fastqc.zip 1SN_13A_2_fastqc.html 1SN_13A_2_fastqc.zip 1SN_14A_1_fastqc.html 1SN_14A_1_fastqc.zip 1SN_14A_2_fastqc.html 1SN_14A_2_fastqc.zip 1SN_15A_1_fastqc.html 1SN_15A_1_fastqc.zip 1SN_15A_2_fastqc.html 1SN_15A_2_fastqc.zip 1SN_16A_1_fastqc.html 1SN_16A_1_fastqc.zip 1SN_16A_2_fastqc.html 1SN_16A_2_fastqc.zip 1SN_17A_1_fastqc.html 1SN_17A_1_fastqc.zip 1SN_17A_2_fastqc.html 1SN_17A_2_fastqc.zip 1SN_18A_1_fastqc.html 1SN_18A_1_fastqc.zip 1SN_18A_2_fastqc.html 1SN_18A_2_fastqc.zip 1SN_19A_1_fastqc.html 1SN_19A_1_fastqc.zip 1SN_19A_2_fastqc.html 1SN_19A_2_fastqc.zip 1SN_1A_1_fastqc.html 1SN_1A_1_fastqc.zip 1SN_1A_2_fastqc.html 1SN_1A_2_fastqc.zip 1SN_20A_1_fastqc.html 1SN_20A_1_fastqc.zip 1SN_20A_2_fastqc.html 1SN_20A_2_fastqc.zip 1SN_21A_1_fastqc.html 1SN_21A_1_fastqc.zip 1SN_21A_2_fastqc.html 1SN_21A_2_fastqc.zip 1SN_22A_1_fastqc.html 1SN_22A_1_fastqc.zip 1SN_22A_2_fastqc.html 1SN_22A_2_fastqc.zip 1SN_23A_1_fastqc.html 1SN_23A_1_fastqc.zip 1SN_23A_2_fastqc.html 1SN_23A_2_fastqc.zip 1SN_24A_1_fastqc.html 1SN_24A_1_fastqc.zip 1SN_24A_2_fastqc.html 1SN_24A_2_fastqc.zip 1SN_25A_1_fastqc.html 1SN_25A_1_fastqc.zip 1SN_25A_2_fastqc.html 1SN_25A_2_fastqc.zip 1SN_26A_1_fastqc.html 1SN_26A_1_fastqc.zip 1SN_26A_2_fastqc.html 1SN_26A_2_fastqc.zip 1SN_27A_1_fastqc.html 1SN_27A_1_fastqc.zip 1SN_27A_2_fastqc.html 1SN_27A_2_fastqc.zip 1SN_28A_1_fastqc.html 1SN_28A_1_fastqc.zip 1SN_28A_2_fastqc.html 1SN_28A_2_fastqc.zip 1SN_29A_1_fastqc.html 1SN_29A_1_fastqc.zip 1SN_29A_2_fastqc.html 1SN_29A_2_fastqc.zip 1SN_2A_1_fastqc.html 1SN_2A_1_fastqc.zip 1SN_2A_2_fastqc.html 1SN_2A_2_fastqc.zip 1SN_30A_1_fastqc.html 1SN_30A_1_fastqc.zip 1SN_30A_2_fastqc.html 1SN_30A_2_fastqc.zip 1SN_31A_1_fastqc.html 1SN_31A_1_fastqc.zip 1SN_31A_2_fastqc.html 1SN_31A_2_fastqc.zip 1SN_32A_1_fastqc.html 1SN_32A_1_fastqc.zip 1SN_32A_2_fastqc.html 1SN_32A_2_fastqc.zip 1SN_3A_1_fastqc.html 1SN_3A_1_fastqc.zip 1SN_3A_2_fastqc.html 1SN_3A_2_fastqc.zip 1SN_4A_1_fastqc.html 1SN_4A_1_fastqc.zip 1SN_4A_2_fastqc.html 1SN_4A_2_fastqc.zip 1SN_5A_1_fastqc.html 1SN_5A_1_fastqc.zip 1SN_5A_2_fastqc.html 1SN_5A_2_fastqc.zip 1SN_6A_1_fastqc.html 1SN_6A_1_fastqc.zip 1SN_6A_2_fastqc.html 1SN_6A_2_fastqc.zip 1SN_7A_1_fastqc.html 1SN_7A_1_fastqc.zip 1SN_7A_2_fastqc.html 1SN_7A_2_fastqc.zip 1SN_8A_1_fastqc.html 1SN_8A_1_fastqc.zip 1SN_8A_2_fastqc.html 1SN_8A_2_fastqc.zip 1SN_9A_1_fastqc.html 1SN_9A_1_fastqc.zip 1SN_9A_2_fastqc.html 1SN_9A_2_fastqc.zip outputtest.txt owl_checksums.md5 temp_checksums.md5
%%bash
ls --ignore="*.gz" /owl_web/nightingales/O_lurida/20160223_gbs/
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc 1HL_10A_1_fastqc 1HL_10A_2_fastqc 1HL_11A_1_fastqc 1HL_11A_2_fastqc 1HL_12A_1_fastqc 1HL_12A_2_fastqc 1HL_13A_1_fastqc 1HL_13A_2_fastqc 1HL_14A_1_fastqc 1HL_14A_2_fastqc 1HL_15A_1_fastqc 1HL_15A_2_fastqc 1HL_16A_1_fastqc 1HL_16A_2_fastqc 1HL_17A_1_fastqc 1HL_17A_2_fastqc 1HL_19A_1_fastqc 1HL_19A_2_fastqc 1HL_1A_1_fastqc 1HL_1A_2_fastqc 1HL_20A_1_fastqc 1HL_20A_2_fastqc 1HL_21A_1_fastqc 1HL_21A_2_fastqc 1HL_22A_1_fastqc 1HL_22A_2_fastqc 1HL_23A_1_fastqc 1HL_23A_2_fastqc 1HL_24A_1_fastqc 1HL_24A_2_fastqc 1HL_25A_1_fastqc 1HL_25A_2_fastqc 1HL_26A_1_fastqc 1HL_26A_2_fastqc 1HL_27A_1_fastqc 1HL_27A_2_fastqc 1HL_28A_1_fastqc 1HL_28A_2_fastqc 1HL_29A_1_fastqc 1HL_29A_2_fastqc 1HL_2A_1_fastqc 1HL_2A_2_fastqc 1HL_31A_1_fastqc 1HL_31A_2_fastqc 1HL_33A_1_fastqc 1HL_33A_2_fastqc 1HL_34A_1_fastqc 1HL_34A_2_fastqc 1HL_35A_1_fastqc 1HL_35A_2_fastqc 1HL_3A_1_fastqc 1HL_3A_2_fastqc 1HL_4A_1_fastqc 1HL_4A_2_fastqc 1HL_5A_1_fastqc 1HL_5A_2_fastqc 1HL_6A_1_fastqc 1HL_6A_2_fastqc 1HL_7A_1_fastqc 1HL_7A_2_fastqc 1HL_8A_1_fastqc 1HL_8A_2_fastqc 1HL_9A_1_fastqc 1HL_9A_2_fastqc 1NF_10A_1_fastqc 1NF_10A_2_fastqc 1NF_11A_1_fastqc 1NF_11A_2_fastqc 1NF_12A_1_fastqc 1NF_12A_2_fastqc 1NF_13A_1_fastqc 1NF_13A_2_fastqc 1NF_14A_1_fastqc 1NF_14A_2_fastqc 1NF_15A_1_fastqc 1NF_15A_2_fastqc 1NF_16A_1_fastqc 1NF_16A_2_fastqc 1NF_17A_1_fastqc 1NF_17A_2_fastqc 1NF_18A_1_fastqc 1NF_18A_2_fastqc 1NF_19A_1_fastqc 1NF_19A_2_fastqc 1NF_1A_1_fastqc 1NF_1A_2_fastqc 1NF_20A_1_fastqc 1NF_20A_2_fastqc 1NF_21A_1_fastqc 1NF_21A_2_fastqc 1NF_22A_1_fastqc 1NF_22A_2_fastqc 1NF_23A_1_fastqc 1NF_23A_2_fastqc 1NF_24A_1_fastqc 1NF_24A_2_fastqc 1NF_25A_1_fastqc 1NF_25A_2_fastqc 1NF_26A_1_fastqc 1NF_26A_2_fastqc 1NF_27A_1_fastqc 1NF_27A_2_fastqc 1NF_28A_1_fastqc 1NF_28A_2_fastqc 1NF_29A_1_fastqc 1NF_29A_2_fastqc 1NF_2A_1_fastqc 1NF_2A_2_fastqc 1NF_30A_1_fastqc 1NF_30A_2_fastqc 1NF_31A_1_fastqc 1NF_31A_2_fastqc 1NF_32A_1_fastqc 1NF_32A_2_fastqc 1NF_33A_1_fastqc 1NF_33A_2_fastqc 1NF_4A_1_fastqc 1NF_4A_2_fastqc 1NF_5A_1_fastqc 1NF_5A_2_fastqc 1NF_6A_1_fastqc 1NF_6A_2_fastqc 1NF_7A_1_fastqc 1NF_7A_2_fastqc 1NF_8A_1_fastqc 1NF_8A_2_fastqc 1NF_9A_1_fastqc 1NF_9A_2_fastqc 1SN_10A_1_fastqc 1SN_10A_2_fastqc 1SN_11A_1_fastqc 1SN_11A_2_fastqc 1SN_12A_1_fastqc 1SN_12A_2_fastqc 1SN_13A_1_fastqc 1SN_13A_2_fastqc 1SN_14A_1_fastqc 1SN_14A_2_fastqc 1SN_15A_1_fastqc 1SN_15A_2_fastqc 1SN_16A_1_fastqc 1SN_16A_2_fastqc 1SN_17A_1_fastqc 1SN_17A_2_fastqc 1SN_18A_1_fastqc 1SN_18A_2_fastqc 1SN_19A_1_fastqc 1SN_19A_2_fastqc 1SN_1A_1_fastqc 1SN_1A_2_fastqc 1SN_20A_1_fastqc 1SN_20A_2_fastqc 1SN_21A_1_fastqc 1SN_21A_2_fastqc 1SN_22A_1_fastqc 1SN_22A_2_fastqc 1SN_23A_1_fastqc 1SN_23A_2_fastqc 1SN_24A_1_fastqc 1SN_24A_2_fastqc 1SN_25A_1_fastqc 1SN_25A_2_fastqc 1SN_26A_1_fastqc 1SN_26A_2_fastqc 1SN_27A_1_fastqc 1SN_27A_2_fastqc 1SN_28A_1_fastqc 1SN_28A_2_fastqc 1SN_29A_1_fastqc 1SN_29A_2_fastqc 1SN_2A_1_fastqc 1SN_2A_2_fastqc 1SN_30A_1_fastqc 1SN_30A_2_fastqc 1SN_31A_1_fastqc 1SN_31A_2_fastqc 1SN_32A_1_fastqc 1SN_32A_2_fastqc 1SN_3A_1_fastqc 1SN_3A_2_fastqc 1SN_4A_1_fastqc 1SN_4A_2_fastqc 1SN_5A_1_fastqc 1SN_5A_2_fastqc 1SN_6A_1_fastqc 1SN_6A_2_fastqc 1SN_7A_1_fastqc 1SN_7A_2_fastqc 1SN_8A_1_fastqc 1SN_8A_2_fastqc 1SN_9A_1_fastqc 1SN_9A_2_fastqc checksums.md5 index.lst md5.check md5.txt md51.txt readme.md split.sh
%%bash
ls /owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc
Icons Images fastqc.fo fastqc_data.txt fastqc_report.html summary.txt
Now, let's move the HTML files.
%%bash
mv *.html /owl_web/nightingales/O_lurida/20160223_gbs/
%%bash
ls /owl_web/nightingales/O_lurida/20160223_gbs/*.html
/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_6A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_6A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_7A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_7A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_8A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_8A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_9A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1HL_9A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_10A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_10A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_11A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_11A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_12A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_12A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_13A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_13A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_14A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_14A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_15A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_15A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_16A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_16A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_17A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_17A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_18A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_18A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_19A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_19A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_1A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_1A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_20A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_20A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_21A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_21A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_22A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_22A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_23A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_23A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_24A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_24A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_25A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_25A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_26A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_26A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_27A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_27A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_28A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_28A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html /owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html
Everything looks good! Let's get rid of the clutter we created on Ostrich for this analsysis.
cd /data/
/data
ls
20161117_oly_gbs_vcf_analysis/ test_file10.txt.gz test_file7.txt.gz 20170227_jay_data_tmp/ test_file2.txt.gz test_file8.txt.gz 20170301_fastqc_gbs/ test_file3.txt.gz test_file9.txt.gz 20170306_fastqc_gbs/ test_file4.txt.gz wgetrc_berk_seq md5s.txt test_file5.txt.gz test_file1.txt.gz test_file6.txt.gz
%%bash
rm -rf 20170306_fastqc_gbs/
ls
20161117_oly_gbs_vcf_analysis/ test_file10.txt.gz test_file6.txt.gz 20170227_jay_data_tmp/ test_file2.txt.gz test_file7.txt.gz 20170301_fastqc_gbs/ test_file3.txt.gz test_file8.txt.gz md5s.txt test_file4.txt.gz test_file9.txt.gz test_file1.txt.gz test_file5.txt.gz wgetrc_berk_seq
Let's generate a list of markdown-formatted links for all of the HTML files.
%%bash
for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html
do
printf "- [%s](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/%s)" "$html" "$html"
done
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: invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments] bash: line 3: printf: - : invalid option printf: usage: printf [-v var] format [arguments]
Well, the hyphen caused an issue. Let's try to escape the hyphen so it's not interpreted as an option indicator.
%%bash
for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html
do
printf "\- [%s](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/%s)" "$html" "$html"
done
\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_2_fastqc.html)\- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html)\- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html)\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html)\- 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That didn't work, as the backslash is interpreted literally.
I'm doing this incorrectly. I should be specifying the print format and then providing printf with the junk I want printed...
The code below tells printf to print four strings in a row, followed by a newline. The %s indicates a string should printed in this position. The list of possible strings (each item in the list is contained in quotes and separated from other items by a space) is supplied after the format layout. The list is "consumed" in order (i.e. The first %s uses the first string in the list. That string is then removed from the list and the list is shifted to the left).
%%bash
for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html
do
printf "%s%s%s%s\n" "- " "[$html]" "(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/" "$html"
done
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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html
Closer... But, it turns out that the for loop is storing the entire path for each file in the html variable. I only want the file name.
The command below uses parameter substitution (${html##*/})to delete the path from the value stored in the html variable (i.e. it deletes everything before, and including, the last forward slash from the value stored in the html variable).
%%bash
for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html
do
printf "%s%s%s%s\n" \
"- " "[$html]" "(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/" "${html##*/}" ")"
done
- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html ) - 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[/owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_2A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_2A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_30A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_30A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_31A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_31A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_32A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_32A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_33A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_33A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_4A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_4A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_5A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_5A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_6A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_6A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_7A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_7A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_8A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_8A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_9A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_9A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_17A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_18A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_18A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_19A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html ) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html )
Much closer... But, I forgot to add an additional %s to the printf format to account for the addition of the ")" that I added to the list of strings.
%%bash
for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html
do
printf "%s%s%s%s%s\n" \
"- " "[$html]" "(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/" "${html##*/}" ")"
done
- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html) - 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html) - [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html)
OMG! So, so close. I want the output to just display the filename for the link; not the full file path. Put another parameter substitution and this should work the way I wanted...
%%bash
for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html
do
printf "%s%s%s%s%s\n" \
"- " "[" ""${html##*/}"" "]" "(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/" "${html##*/}" ")"
done
- [1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_10A_1_fastqc.html) - [1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_10A_2_fastqc.html) - [1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_11A_1_fastqc.html) - [1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_11A_2_fastqc.html) - [1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_12A_1_fastqc.html) - [1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_12A_2_fastqc.html) - [1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_13A_1_fastqc.html) - [1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_13A_2_fastqc.html) - [1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_14A_1_fastqc.html) - [1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_14A_2_fastqc.html) - [1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_15A_1_fastqc.html) - [1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_15A_2_fastqc.html) - [1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_16A_1_fastqc.html) - [1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_16A_2_fastqc.html) - [1HL_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_17A_1_fastqc.html) - [1HL_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_17A_2_fastqc.html) - [1HL_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_19A_1_fastqc.html) - [1HL_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_19A_2_fastqc.html) - [1HL_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_1A_1_fastqc.html) - [1HL_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_1A_2_fastqc.html) - [1HL_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_20A_1_fastqc.html) - [1HL_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_20A_2_fastqc.html) - [1HL_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_21A_1_fastqc.html) - [1HL_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_21A_2_fastqc.html) - [1HL_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_22A_1_fastqc.html) - [1HL_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_22A_2_fastqc.html) - [1HL_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_23A_1_fastqc.html) - [1HL_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_23A_2_fastqc.html) - [1HL_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_24A_1_fastqc.html) - [1HL_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_24A_2_fastqc.html) - [1HL_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_25A_1_fastqc.html) - [1HL_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_25A_2_fastqc.html) - [1HL_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_26A_1_fastqc.html) - [1HL_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_26A_2_fastqc.html) - [1HL_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_27A_1_fastqc.html) - [1HL_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_27A_2_fastqc.html) - [1HL_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_28A_1_fastqc.html) - [1HL_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_28A_2_fastqc.html) - [1HL_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_29A_1_fastqc.html) - [1HL_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_29A_2_fastqc.html) - [1HL_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_2A_1_fastqc.html) - [1HL_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_2A_2_fastqc.html) - [1HL_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_31A_1_fastqc.html) - [1HL_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_31A_2_fastqc.html) - [1HL_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_33A_1_fastqc.html) - [1HL_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_33A_2_fastqc.html) - [1HL_34A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_34A_1_fastqc.html) - [1HL_34A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_34A_2_fastqc.html) - [1HL_35A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_35A_1_fastqc.html) - [1HL_35A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_35A_2_fastqc.html) - [1HL_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_3A_1_fastqc.html) - [1HL_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_3A_2_fastqc.html) - [1HL_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_4A_1_fastqc.html) - [1HL_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_4A_2_fastqc.html) - [1HL_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_5A_1_fastqc.html) - [1HL_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_5A_2_fastqc.html) - [1HL_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_6A_1_fastqc.html) - [1HL_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_6A_2_fastqc.html) - [1HL_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_7A_1_fastqc.html) - [1HL_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_7A_2_fastqc.html) - [1HL_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_8A_1_fastqc.html) - [1HL_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_8A_2_fastqc.html) - [1HL_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_9A_1_fastqc.html) - [1HL_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1HL_9A_2_fastqc.html) - [1NF_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_10A_1_fastqc.html) - [1NF_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_10A_2_fastqc.html) - [1NF_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_11A_1_fastqc.html) - [1NF_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_11A_2_fastqc.html) - [1NF_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_12A_1_fastqc.html) - [1NF_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_12A_2_fastqc.html) - [1NF_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_13A_1_fastqc.html) - [1NF_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_13A_2_fastqc.html) - [1NF_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_14A_1_fastqc.html) - [1NF_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_14A_2_fastqc.html) - [1NF_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_15A_1_fastqc.html) - [1NF_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_15A_2_fastqc.html) - [1NF_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_16A_1_fastqc.html) - [1NF_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_16A_2_fastqc.html) - [1NF_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_17A_1_fastqc.html) - [1NF_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_17A_2_fastqc.html) - [1NF_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_18A_1_fastqc.html) - [1NF_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_18A_2_fastqc.html) - [1NF_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_19A_1_fastqc.html) - [1NF_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_19A_2_fastqc.html) - [1NF_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_1A_1_fastqc.html) - [1NF_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_1A_2_fastqc.html) - [1NF_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_20A_1_fastqc.html) - [1NF_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_20A_2_fastqc.html) - [1NF_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_21A_1_fastqc.html) - [1NF_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_21A_2_fastqc.html) - [1NF_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_22A_1_fastqc.html) - [1NF_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_22A_2_fastqc.html) - [1NF_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_23A_1_fastqc.html) - [1NF_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_23A_2_fastqc.html) - [1NF_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_24A_1_fastqc.html) - [1NF_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_24A_2_fastqc.html) - [1NF_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_25A_1_fastqc.html) - [1NF_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_25A_2_fastqc.html) - [1NF_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_26A_1_fastqc.html) - [1NF_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_26A_2_fastqc.html) - [1NF_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_27A_1_fastqc.html) - [1NF_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_27A_2_fastqc.html) - [1NF_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_28A_1_fastqc.html) - [1NF_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_28A_2_fastqc.html) - [1NF_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_29A_1_fastqc.html) - [1NF_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_29A_2_fastqc.html) - [1NF_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_2A_1_fastqc.html) - [1NF_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_2A_2_fastqc.html) - [1NF_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_30A_1_fastqc.html) - [1NF_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_30A_2_fastqc.html) - [1NF_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_31A_1_fastqc.html) - [1NF_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_31A_2_fastqc.html) - [1NF_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_32A_1_fastqc.html) - [1NF_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_32A_2_fastqc.html) - [1NF_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_33A_1_fastqc.html) - [1NF_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_33A_2_fastqc.html) - [1NF_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_4A_1_fastqc.html) - [1NF_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_4A_2_fastqc.html) - [1NF_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_5A_1_fastqc.html) - [1NF_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_5A_2_fastqc.html) - [1NF_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_6A_1_fastqc.html) - [1NF_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_6A_2_fastqc.html) - [1NF_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_7A_1_fastqc.html) - [1NF_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_7A_2_fastqc.html) - [1NF_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_8A_1_fastqc.html) - [1NF_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_8A_2_fastqc.html) - [1NF_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_9A_1_fastqc.html) - [1NF_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1NF_9A_2_fastqc.html) - [1SN_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_10A_1_fastqc.html) - [1SN_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_10A_2_fastqc.html) - [1SN_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_11A_1_fastqc.html) - [1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_11A_2_fastqc.html) - [1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_12A_1_fastqc.html) - [1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_12A_2_fastqc.html) - [1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_13A_1_fastqc.html) - [1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_13A_2_fastqc.html) - [1SN_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_14A_1_fastqc.html) - [1SN_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_14A_2_fastqc.html) - [1SN_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_15A_1_fastqc.html) - [1SN_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_15A_2_fastqc.html) - [1SN_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_16A_1_fastqc.html) - [1SN_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_16A_2_fastqc.html) - [1SN_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_17A_1_fastqc.html) - [1SN_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_17A_2_fastqc.html) - [1SN_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_18A_1_fastqc.html) - [1SN_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_18A_2_fastqc.html) - [1SN_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_19A_1_fastqc.html) - [1SN_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_19A_2_fastqc.html) - [1SN_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_1A_1_fastqc.html) - [1SN_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_1A_2_fastqc.html) - [1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_20A_1_fastqc.html) - [1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_20A_2_fastqc.html) - [1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_21A_1_fastqc.html) - [1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_21A_2_fastqc.html) - [1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_22A_1_fastqc.html) - [1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_22A_2_fastqc.html) - [1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_23A_1_fastqc.html) - [1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_23A_2_fastqc.html) - [1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_24A_1_fastqc.html) - [1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_24A_2_fastqc.html) - [1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_25A_1_fastqc.html) - [1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_25A_2_fastqc.html) - [1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_26A_1_fastqc.html) - [1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_26A_2_fastqc.html) - [1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_27A_1_fastqc.html) - [1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_27A_2_fastqc.html) - [1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_28A_1_fastqc.html) - [1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_28A_2_fastqc.html) - [1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_29A_1_fastqc.html) - [1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_29A_2_fastqc.html) - [1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_2A_1_fastqc.html) - [1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_2A_2_fastqc.html) - [1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_30A_1_fastqc.html) - [1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_30A_2_fastqc.html) - [1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_31A_1_fastqc.html) - [1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_31A_2_fastqc.html) - [1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_32A_1_fastqc.html) - [1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_32A_2_fastqc.html) - [1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_3A_1_fastqc.html) - [1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_3A_2_fastqc.html) - [1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_4A_1_fastqc.html) - [1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_4A_2_fastqc.html) - [1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_5A_1_fastqc.html) - [1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_5A_2_fastqc.html) - [1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_6A_1_fastqc.html) - [1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_6A_2_fastqc.html) - [1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_7A_1_fastqc.html) - [1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_7A_2_fastqc.html) - [1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_8A_1_fastqc.html) - [1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_8A_2_fastqc.html) - [1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_9A_1_fastqc.html) - [1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/ 1SN_9A_2_fastqc.html)
At last! Here are the links to all of the FastQC reports!
1HL_10A_1_fastqc.html)
1HL_10A_2_fastqc.html)
1HL_11A_1_fastqc.html)
1HL_11A_2_fastqc.html)
1HL_12A_1_fastqc.html)
1HL_12A_2_fastqc.html)
1HL_13A_1_fastqc.html)
1HL_13A_2_fastqc.html)
1HL_14A_1_fastqc.html)
1HL_14A_2_fastqc.html)
1HL_15A_1_fastqc.html)
1HL_15A_2_fastqc.html)
1HL_16A_1_fastqc.html)
1HL_16A_2_fastqc.html)
1HL_17A_1_fastqc.html)
1HL_17A_2_fastqc.html)
1HL_19A_1_fastqc.html)
1HL_19A_2_fastqc.html)
1HL_1A_1_fastqc.html)
1HL_1A_2_fastqc.html)
1HL_20A_1_fastqc.html)
1HL_20A_2_fastqc.html)
1HL_21A_1_fastqc.html)
1HL_21A_2_fastqc.html)
1HL_22A_1_fastqc.html)
1HL_22A_2_fastqc.html)
1HL_23A_1_fastqc.html)
1HL_23A_2_fastqc.html)
1HL_24A_1_fastqc.html)
1HL_24A_2_fastqc.html)
1HL_25A_1_fastqc.html)
1HL_25A_2_fastqc.html)
1HL_26A_1_fastqc.html)
1HL_26A_2_fastqc.html)
1HL_27A_1_fastqc.html)
1HL_27A_2_fastqc.html)
1HL_28A_1_fastqc.html)
1HL_28A_2_fastqc.html)
1HL_29A_1_fastqc.html)
1HL_29A_2_fastqc.html)
1HL_2A_1_fastqc.html)
1HL_2A_2_fastqc.html)
1HL_31A_1_fastqc.html)
1HL_31A_2_fastqc.html)
1HL_33A_1_fastqc.html)
1HL_33A_2_fastqc.html)
1HL_34A_1_fastqc.html)
1HL_34A_2_fastqc.html)
1HL_35A_1_fastqc.html)
1HL_35A_2_fastqc.html)
1HL_3A_1_fastqc.html)
1HL_3A_2_fastqc.html)
1HL_4A_1_fastqc.html)
1HL_4A_2_fastqc.html)
1HL_5A_1_fastqc.html)
1HL_5A_2_fastqc.html)
1HL_6A_1_fastqc.html)
1HL_6A_2_fastqc.html)
1HL_7A_1_fastqc.html)
1HL_7A_2_fastqc.html)
1HL_8A_1_fastqc.html)
1HL_8A_2_fastqc.html)
1HL_9A_1_fastqc.html)
1HL_9A_2_fastqc.html)
1NF_10A_1_fastqc.html)
1NF_10A_2_fastqc.html)
1NF_11A_1_fastqc.html)
1NF_11A_2_fastqc.html)
1NF_12A_1_fastqc.html)
1NF_12A_2_fastqc.html)
1NF_13A_1_fastqc.html)
1NF_13A_2_fastqc.html)
1NF_14A_1_fastqc.html)
1NF_14A_2_fastqc.html)
1NF_15A_1_fastqc.html)
1NF_15A_2_fastqc.html)
1NF_16A_1_fastqc.html)
1NF_16A_2_fastqc.html)
1NF_17A_1_fastqc.html)
1NF_17A_2_fastqc.html)
1NF_18A_1_fastqc.html)
1NF_18A_2_fastqc.html)
1NF_19A_1_fastqc.html)
1NF_19A_2_fastqc.html)
1NF_1A_1_fastqc.html)
1NF_1A_2_fastqc.html)
1NF_20A_1_fastqc.html)
1NF_20A_2_fastqc.html)
1NF_21A_1_fastqc.html)
1NF_21A_2_fastqc.html)
1NF_22A_1_fastqc.html)
1NF_22A_2_fastqc.html)
1NF_23A_1_fastqc.html)
1NF_23A_2_fastqc.html)
1NF_24A_1_fastqc.html)
1NF_24A_2_fastqc.html)
1NF_25A_1_fastqc.html)
1NF_25A_2_fastqc.html)
1NF_26A_1_fastqc.html)
1NF_26A_2_fastqc.html)
1NF_27A_1_fastqc.html)
1NF_27A_2_fastqc.html)
1NF_28A_1_fastqc.html)
1NF_28A_2_fastqc.html)
1NF_29A_1_fastqc.html)
1NF_29A_2_fastqc.html)
1NF_2A_1_fastqc.html)
1NF_2A_2_fastqc.html)
1NF_30A_1_fastqc.html)
1NF_30A_2_fastqc.html)
1NF_31A_1_fastqc.html)
1NF_31A_2_fastqc.html)
1NF_32A_1_fastqc.html)
1NF_32A_2_fastqc.html)
1NF_33A_1_fastqc.html)
1NF_33A_2_fastqc.html)
1NF_4A_1_fastqc.html)
1NF_4A_2_fastqc.html)
1NF_5A_1_fastqc.html)
1NF_5A_2_fastqc.html)
1NF_6A_1_fastqc.html)
1NF_6A_2_fastqc.html)
1NF_7A_1_fastqc.html)
1NF_7A_2_fastqc.html)
1NF_8A_1_fastqc.html)
1NF_8A_2_fastqc.html)
1NF_9A_1_fastqc.html)
1NF_9A_2_fastqc.html)
1SN_10A_1_fastqc.html)
1SN_10A_2_fastqc.html)
1SN_11A_1_fastqc.html)
1SN_11A_2_fastqc.html)
1SN_12A_1_fastqc.html)
1SN_12A_2_fastqc.html)
1SN_13A_1_fastqc.html)
1SN_13A_2_fastqc.html)
1SN_14A_1_fastqc.html)
1SN_14A_2_fastqc.html)
1SN_15A_1_fastqc.html)
1SN_15A_2_fastqc.html)
1SN_16A_1_fastqc.html)
1SN_16A_2_fastqc.html)
1SN_17A_1_fastqc.html)
1SN_17A_2_fastqc.html)
1SN_18A_1_fastqc.html)
1SN_18A_2_fastqc.html)
1SN_19A_1_fastqc.html)
1SN_19A_2_fastqc.html)
1SN_1A_1_fastqc.html)
1SN_1A_2_fastqc.html)
1SN_20A_1_fastqc.html)
1SN_20A_2_fastqc.html)
1SN_21A_1_fastqc.html)
1SN_21A_2_fastqc.html)
1SN_22A_1_fastqc.html)
1SN_22A_2_fastqc.html)
1SN_23A_1_fastqc.html)
1SN_23A_2_fastqc.html)
1SN_24A_1_fastqc.html)
1SN_24A_2_fastqc.html)
1SN_25A_1_fastqc.html)
1SN_25A_2_fastqc.html)
1SN_26A_1_fastqc.html)
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1SN_27A_1_fastqc.html)
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1SN_28A_1_fastqc.html)
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1SN_29A_1_fastqc.html)
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1SN_2A_1_fastqc.html)
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1SN_30A_1_fastqc.html)
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1SN_31A_1_fastqc.html)
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1SN_32A_1_fastqc.html)
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1SN_3A_1_fastqc.html)
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1SN_4A_1_fastqc.html)
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1SN_5A_1_fastqc.html)
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1SN_6A_1_fastqc.html)
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1SN_7A_1_fastqc.html)
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1SN_8A_1_fastqc.html)
1SN_8A_2_fastqc.html)
1SN_9A_1_fastqc.html)
1SN_9A_2_fastqc.html)