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 20 22:17:40 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
cd /gitrepos/Reseqtools/iTools_Code/
/gitrepos/Reseqtools/iTools_Code
Check for raw FASTQ files
ls /data/oly_gbs_raw/
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz index.lst split.sh 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz split/ split2/
Verify index file looks OK.
%%bash
head /data/oly_gbs_raw/index.lst
OYSzenG1AAD96FAAPEI-109 CTCC 1NF_1A OYSzenG1AAD96FAAPEI-109 TGCA 1NF_2A OYSzenG1AAD96FAAPEI-109 ACTA 1NF_4A OYSzenG1AAD96FAAPEI-109 CAGA 1NF_5A OYSzenG1AAD96FAAPEI-109 AACT 1NF_6A OYSzenG1AAD96FAAPEI-109 GCGT 1NF_7A OYSzenG1AAD96FAAPEI-109 CGAT 1NF_8A OYSzenG1AAD96FAAPEI-109 GTAA 1NF_9A OYSzenG1AAD96FAAPEI-109 AGGC 1NF_10A OYSzenG1AAD96FAAPEI-109 GATC 1NF_11A
Whoops! That's not right! I forgot I moved the corrected files to my paper repo...
ls /gitrepos/paper_oly_gbs/data/
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/ SNP.stat.xls 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.html enzyme.txt 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/ index.lst 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.html readme.md Data.stat.xls split.sh
%%bash
head /gitrepos/paper_oly_gbs/data/index.lst
head /gitrepos/paper_oly_gbs/data/enzyme.txt
1NF_1A CTCC 1NF_2A TGCA 1NF_4A ACTA 1NF_5A CAGA 1NF_6A AACT 1NF_7A GCGT 1NF_8A CGAT 1NF_9A GTAA 1NF_10A AGGC 1NF_11A GATC CAGC CTGC
Looks good!
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/dataenzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split/
Process is interrupted.
Ugh. Ran it to the same directory as I did the last time I ran the script! Need to change to a different directory...
This also means that some of the files from the first run are probably screwed up!
However, the goal of this is to compare a subset of the output and see if the two runs produced different results. Don't need all the files in order to do that comparison.
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/dataenzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split2/
real 559m41.229s user 392m10.870s sys 145m5.860s
%%bash
ls -lh /data/oly_gbs_raw/split/ | head
total 130M -rw-r--r-- 1 srlab staff 0 Mar 20 22:22 1HL_10A_1.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:22 1HL_10A_2.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_11A_1.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_11A_2.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_12A_1.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_12A_2.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_13A_1.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_13A_2.fq.gz -rw-r--r-- 1 srlab staff 0 Mar 20 22:23 1HL_14A_1.fq.gz
ls: write error: Broken pipe
Nope. I screwed it up. The demultplexing I ran in Step 9 overwrote everything from the first run!
Well, let's run it again so we have files to compare...
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/dataenzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split/
real 571m24.244s user 398m52.700s sys 145m14.710s
Arrived to lab this morning to disconnects errors. Let's see if these worked...
%%bash
ls -lh /data/oly_gbs_raw/split/ | head
total 37G -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_10A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_10A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_11A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_11A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_12A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_12A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_13A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_13A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 17:16 1HL_14A_1.fq.gz
ls: write error: Broken pipe
%%bash
date
Tue Mar 21 18:47:32 UTC 2017
%%bash
ls -lh /data/oly_gbs_raw/split2/
total 37G -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_10A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_10A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_11A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_11A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_12A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_12A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_13A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_13A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_14A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_14A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_15A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_15A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_16A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_16A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_17A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_17A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_19A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_19A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_1A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_1A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_20A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_20A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_21A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_21A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_22A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_22A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_23A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_23A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_24A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_24A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_25A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_25A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_26A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_26A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_27A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_27A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_28A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_28A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_29A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_29A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_2A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_2A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_31A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_31A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_33A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_33A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_34A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_34A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_35A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_35A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_3A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_3A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_4A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_4A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_5A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_5A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_6A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_6A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_7A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_7A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_8A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_8A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_9A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1HL_9A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_10A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_10A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_11A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_11A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_12A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_12A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_13A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_13A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_14A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_14A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_15A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_15A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_16A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_16A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_17A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_17A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_18A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_18A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_19A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_19A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_1A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_1A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_20A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_20A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_21A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_21A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_22A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_22A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_23A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_23A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_24A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_24A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_25A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_25A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_26A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_26A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_27A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_27A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_28A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_28A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_29A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_29A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_2A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_2A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_30A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_30A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_31A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_31A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_32A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_32A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_33A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_33A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_4A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_4A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_5A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_5A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_6A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_6A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_7A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_7A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_8A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_8A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_9A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1NF_9A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_10A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_10A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_11A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_11A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_12A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_12A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_13A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_13A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_14A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_14A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_15A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_15A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_16A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_16A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_17A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_17A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_18A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_18A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_19A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_19A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_1A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_1A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_20A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_20A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_21A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_21A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_22A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_22A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_23A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_23A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_24A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_24A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_25A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_25A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_26A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_26A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_27A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_27A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_28A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_28A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_29A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_29A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_2A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_2A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_30A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_30A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_31A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_31A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_32A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_32A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_3A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_3A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_4A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_4A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_5A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_5A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_6A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_6A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_7A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_7A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_8A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_8A_2.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_9A_1.fq.gz -rw-r--r-- 1 srlab staff 20 Mar 21 07:45 1SN_9A_2.fq.gz -rw-r--r-- 1 srlab staff 17G Mar 21 07:45 UnKnow_1.fq.gz -rw-r--r-- 1 srlab staff 20G Mar 21 07:45 UnKnow_2.fq.gz
OMG! There's a typo in the both of the demultiplexing scripts above! The path to the enzyme list is incorrect... :( Let's run them again...
It certainly would be nice if some checks were built into this program (and, it's be nice if I was paying more attention)!
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split2/
bash: line 1: ./iTools: No such file or directory real 0m0.002s user 0m0.000s sys 0m0.000s
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split/
bash: line 1: ./iTools: No such file or directory real 0m0.001s user 0m0.000s sys 0m0.000s
cd /gitrepos/Reseqtools/iTools_Code/
/gitrepos/Reseqtools/iTools_Code
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split/
real 984m39.534s user 799m44.020s sys 151m6.100s
%%bash
time ./iTools Fqtools splitpool \
-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \
-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \
-Index /gitrepos/paper_oly_gbs/data/index.lst \
-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \
-MisMatch \
-OutDir /data/oly_gbs_raw/split2/
real 984m28.356s user 797m9.610s sys 153m32.850s