%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE:
Tue Sep 11 12:47:33 PDT 2018
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.5 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
roadrunner
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Thread(s) per core: 2
Core(s) per socket: 4
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 26
Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz
Stepping: 5
CPU MHz: 2394.000
CPU max MHz: 2394.0000
CPU min MHz: 1596.0000
BogoMIPS: 4521.80
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 8192K
NUMA node0 CPU(s): 0-15
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts nopl xtopology nonstop_tsc aperfmperf eagerfpu pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida
------------
Memory Specs
total used free shared buff/cache available
Mem: 47G 2.1G 9.8G 559M 35G 43G
Swap: 47G 0B 47G
No LSB modules are available.
%%bash
ls /home/sam/data/Cvirginica/concatenated/
20180910_Cvirginica_oil_fastqc 2112_lane1_ACAGTG.fastq.gz 2112_lane1_ATCACG.fastq.gz 2112_lane1_CAGATC.fastq.gz 2112_lane1_GCCAAT.fastq.gz 2112_lane1_TGACCA.fastq.gz 2112_lane1_TTAGGC.fastq.gz
%%bash
mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01
mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc
cd /home/sam/data/Cvirginica/concatenated/
time \
/home/shared/TrimGalore-0.4.5/trim_galore \
--ouput_dir /home/sam/analyses/20180911_virginica_oil_trimgalore_01 \
--fastqc_args \
"--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc \
--threads 16" \
2112_lane1_ACAGTG.fastq.gz \
2112_lane1_ATCACG.fastq.gz \
2112_lane1_CAGATC.fastq.gz \
2112_lane1_GCCAAT.fastq.gz \
2112_lane1_TGACCA.fastq.gz \
2112_lane1_TTAGGC.fastq.gz \
> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stdout.log \
2> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stderr.log
sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 0m0.091s user 0m0.044s sys 0m0.004s
%%bash
tail /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stdout.log
%%bash
tail /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stderr.log
Unknown option: ouput_dir Please respecify command line options
%%bash
mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01
mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc
cd /home/sam/data/Cvirginica/concatenated/
time \
/home/shared/TrimGalore-0.4.5/trim_galore \
--output_dir /home/sam/analyses/20180911_virginica_oil_trimgalore_01 \
--fastqc_args \
"--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc \
--threads 16" \
2112_lane1_ACAGTG.fastq.gz \
2112_lane1_ATCACG.fastq.gz \
2112_lane1_CAGATC.fastq.gz \
2112_lane1_GCCAAT.fastq.gz \
2112_lane1_TGACCA.fastq.gz \
2112_lane1_TTAGGC.fastq.gz \
> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stdout.log \
2> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stderr.log
sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
mkdir: cannot create directory ‘/home/sam/analyses/20180911_virginica_oil_trimgalore_01’: File exists mkdir: cannot create directory ‘/home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc’: File exists real 78m53.332s user 144m38.712s sys 3m52.692s
%%bash
ls /home/sam/analyses/20180911_virginica_oil_trimgalore_01
20180911_trimgalore.stderr.log 20180911_trimgalore.stdout.log 20180911_virginica_oil_trimmed_fastqc 2112_lane1_ACAGTG.fastq.gz_trimming_report.txt 2112_lane1_ACAGTG_trimmed.fq.gz 2112_lane1_ATCACG.fastq.gz_trimming_report.txt 2112_lane1_ATCACG_trimmed.fq.gz 2112_lane1_CAGATC.fastq.gz_trimming_report.txt 2112_lane1_CAGATC_trimmed.fq.gz 2112_lane1_GCCAAT.fastq.gz_trimming_report.txt 2112_lane1_GCCAAT_trimmed.fq.gz 2112_lane1_TGACCA.fastq.gz_trimming_report.txt 2112_lane1_TGACCA_trimmed.fq.gz 2112_lane1_TTAGGC.fastq.gz_trimming_report.txt 2112_lane1_TTAGGC_trimmed.fq.gz
%%bash
ls /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc
2112_lane1_ACAGTG_trimmed_fastqc.html 2112_lane1_ACAGTG_trimmed_fastqc.zip 2112_lane1_ATCACG_trimmed_fastqc.html 2112_lane1_ATCACG_trimmed_fastqc.zip 2112_lane1_CAGATC_trimmed_fastqc.html 2112_lane1_CAGATC_trimmed_fastqc.zip 2112_lane1_GCCAAT_trimmed_fastqc.html 2112_lane1_GCCAAT_trimmed_fastqc.zip 2112_lane1_TGACCA_trimmed_fastqc.html 2112_lane1_TGACCA_trimmed_fastqc.zip 2112_lane1_TTAGGC_trimmed_fastqc.html 2112_lane1_TTAGGC_trimmed_fastqc.zip
%%bash
cd /home/sam/analyses/20180911_virginica_oil_trimgalore_01
multiqc .
cd /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc
multiqc .
sed '/^Subject:/ s/ / multiqc JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
Searching 26 files.. Searching 12 files..
[WARNING] multiqc : MultiQC Version v1.6 now available! [INFO ] multiqc : This is MultiQC v1.5.dev0 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching '.' [INFO ] cutadapt : Found 6 reports [INFO ] fastqc : Found 6 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete [WARNING] multiqc : MultiQC Version v1.6 now available! [INFO ] multiqc : This is MultiQC v1.5.dev0 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching '.' [INFO ] fastqc : Found 6 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete
sudo to copy to Owl outside of notebook¶%%bash
tree /mnt/owl/Athaliana/20180911_virginica_oil_trimgalore_01/
/mnt/owl/Athaliana/20180911_virginica_oil_trimgalore_01/ ├── 20180911_trimgalore.stderr.log ├── 20180911_trimgalore.stdout.log ├── 20180911_virginica_oil_trimmed_fastqc │ ├── 2112_lane1_ACAGTG_trimmed_fastqc.html │ ├── 2112_lane1_ACAGTG_trimmed_fastqc.zip │ ├── 2112_lane1_ATCACG_trimmed_fastqc.html │ ├── 2112_lane1_ATCACG_trimmed_fastqc.zip │ ├── 2112_lane1_CAGATC_trimmed_fastqc.html │ ├── 2112_lane1_CAGATC_trimmed_fastqc.zip │ ├── 2112_lane1_GCCAAT_trimmed_fastqc.html │ ├── 2112_lane1_GCCAAT_trimmed_fastqc.zip │ ├── 2112_lane1_TGACCA_trimmed_fastqc.html │ ├── 2112_lane1_TGACCA_trimmed_fastqc.zip │ ├── 2112_lane1_TTAGGC_trimmed_fastqc.html │ ├── 2112_lane1_TTAGGC_trimmed_fastqc.zip │ ├── multiqc_data │ │ ├── multiqc_data.json │ │ ├── multiqc_fastqc.txt │ │ ├── multiqc_general_stats.txt │ │ ├── multiqc.log │ │ └── multiqc_sources.txt │ └── multiqc_report.html ├── 2112_lane1_ACAGTG.fastq.gz_trimming_report.txt ├── 2112_lane1_ACAGTG_trimmed.fq.gz ├── 2112_lane1_ATCACG.fastq.gz_trimming_report.txt ├── 2112_lane1_ATCACG_trimmed.fq.gz ├── 2112_lane1_CAGATC.fastq.gz_trimming_report.txt ├── 2112_lane1_CAGATC_trimmed.fq.gz ├── 2112_lane1_GCCAAT.fastq.gz_trimming_report.txt ├── 2112_lane1_GCCAAT_trimmed.fq.gz ├── 2112_lane1_TGACCA.fastq.gz_trimming_report.txt ├── 2112_lane1_TGACCA_trimmed.fq.gz ├── 2112_lane1_TTAGGC.fastq.gz_trimming_report.txt ├── 2112_lane1_TTAGGC_trimmed.fq.gz ├── multiqc_data │ ├── multiqc_cutadapt.txt │ ├── multiqc_data.json │ ├── multiqc_fastqc.txt │ ├── multiqc_general_stats.txt │ ├── multiqc.log │ └── multiqc_sources.txt └── multiqc_report.html 3 directories, 39 files