%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
lsb_release -a #Display operating system info
echo ""
echo "------------"
echo "HOSTNAME: "; hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE: Wed May 16 15:00:45 PDT 2018 ------------ Distributor ID: Ubuntu Description: Ubuntu 16.04.4 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: 4521.81 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 pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm retpoline kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida ------------ Memory Specs total used free shared buff/cache available Mem: 47G 421M 3.0G 314M 43G 45G Swap: 47G 281M 47G
No LSB modules are available.
%%bash
mkdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs
mkdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc
cd /home/sam/data/geoduck_EPI
time \
/home/shared/TrimGalore-0.4.5/trim_galore \
--paired \
--rrbs \
--output_dir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs \
--fastqc_args \
"--outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc \
--threads 16" \
EPI-103_S27_L005_R1_001.fastq.gz \
EPI-103_S27_L005_R2_001.fastq.gz \
EPI-104_S28_L005_R1_001.fastq.gz \
EPI-104_S28_L005_R2_001.fastq.gz \
EPI-111_S29_L005_R1_001.fastq.gz \
EPI-111_S29_L005_R2_001.fastq.gz \
EPI-113_S30_L005_R1_001.fastq.gz \
EPI-113_S30_L005_R2_001.fastq.gz \
EPI-119_S31_L005_R1_001.fastq.gz \
EPI-119_S31_L005_R2_001.fastq.gz \
EPI-120_S32_L005_R1_001.fastq.gz \
EPI-120_S32_L005_R2_001.fastq.gz \
EPI-127_S33_L005_R1_001.fastq.gz \
EPI-127_S33_L005_R2_001.fastq.gz \
EPI-128_S34_L005_R1_001.fastq.gz \
EPI-128_S34_L005_R2_001.fastq.gz \
EPI-135_S35_L005_R1_001.fastq.gz \
EPI-135_S35_L005_R2_001.fastq.gz \
EPI-136_S36_L005_R1_001.fastq.gz \
EPI-136_S36_L005_R2_001.fastq.gz \
EPI-143_S37_L005_R1_001.fastq.gz \
EPI-143_S37_L005_R2_001.fastq.gz \
EPI-145_S38_L005_R1_001.fastq.gz \
EPI-145_S38_L005_R2_001.fastq.gz \
EPI-151_S2_L002_R1_001.fastq.gz \
EPI-151_S2_L002_R2_001.fastq.gz \
EPI-152_S3_L002_R1_001.fastq.gz \
EPI-152_S3_L002_R2_001.fastq.gz \
EPI-153_S4_L002_R1_001.fastq.gz \
EPI-153_S4_L002_R2_001.fastq.gz \
EPI-154_S5_L002_R1_001.fastq.gz \
EPI-154_S5_L002_R2_001.fastq.gz \
EPI-159_S6_L002_R1_001.fastq.gz \
EPI-159_S6_L002_R2_001.fastq.gz \
EPI-160_S7_L002_R1_001.fastq.gz \
EPI-160_S7_L002_R2_001.fastq.gz \
EPI-161_S8_L002_R1_001.fastq.gz \
EPI-161_S8_L002_R2_001.fastq.gz \
EPI-162_S9_L002_R1_001.fastq.gz \
EPI-162_S9_L002_R2_001.fastq.gz \
EPI-167_S10_L002_R1_001.fastq.gz \
EPI-167_S10_L002_R2_001.fastq.gz \
EPI-168_S11_L002_R1_001.fastq.gz \
EPI-168_S11_L002_R2_001.fastq.gz \
EPI-169_S12_L002_R1_001.fastq.gz \
EPI-169_S12_L002_R2_001.fastq.gz \
EPI-170_S13_L002_R1_001.fastq.gz \
EPI-170_S13_L002_R2_001.fastq.gz \
EPI-175_S14_L003_R1_001.fastq.gz \
EPI-175_S14_L003_R2_001.fastq.gz \
EPI-176_S15_L003_R1_001.fastq.gz \
EPI-176_S15_L003_R2_001.fastq.gz \
EPI-181_S16_L003_R1_001.fastq.gz \
EPI-181_S16_L003_R2_001.fastq.gz \
EPI-182_S17_L003_R1_001.fastq.gz \
EPI-182_S17_L003_R2_001.fastq.gz \
EPI-184_S18_L003_R1_001.fastq.gz \
EPI-184_S18_L003_R2_001.fastq.gz \
EPI-185_S19_L003_R1_001.fastq.gz \
EPI-185_S19_L003_R2_001.fastq.gz \
EPI-187_S20_L003_R1_001.fastq.gz \
EPI-187_S20_L003_R2_001.fastq.gz \
EPI-188_S21_L003_R1_001.fastq.gz \
EPI-188_S21_L003_R2_001.fastq.gz \
EPI-193_S22_L003_R1_001.fastq.gz \
EPI-193_S22_L003_R2_001.fastq.gz \
EPI-194_S23_L003_R1_001.fastq.gz \
EPI-194_S23_L003_R2_001.fastq.gz \
EPI-199_S24_L003_R1_001.fastq.gz \
EPI-199_S24_L003_R2_001.fastq.gz \
EPI-200_S25_L003_R1_001.fastq.gz \
EPI-200_S25_L003_R2_001.fastq.gz \
EPI-205_S26_L004_R1_001.fastq.gz \
EPI-205_S26_L004_R2_001.fastq.gz \
EPI-206_S27_L004_R1_001.fastq.gz \
EPI-206_S27_L004_R2_001.fastq.gz \
EPI-208_S28_L004_R1_001.fastq.gz \
EPI-208_S28_L004_R2_001.fastq.gz \
EPI-209_S29_L004_R1_001.fastq.gz \
EPI-209_S29_L004_R2_001.fastq.gz \
EPI-214_S30_L004_R1_001.fastq.gz \
EPI-214_S30_L004_R2_001.fastq.gz \
EPI-215_S31_L004_R1_001.fastq.gz \
EPI-215_S31_L004_R2_001.fastq.gz \
EPI-220_S32_L004_R1_001.fastq.gz \
EPI-220_S32_L004_R2_001.fastq.gz \
EPI-221_S33_L004_R1_001.fastq.gz \
EPI-221_S33_L004_R2_001.fastq.gz \
EPI-226_S34_L004_R1_001.fastq.gz \
EPI-226_S34_L004_R2_001.fastq.gz \
EPI-227_S35_L004_R1_001.fastq.gz \
EPI-227_S35_L004_R2_001.fastq.gz \
EPI-229_S36_L004_R1_001.fastq.gz \
EPI-229_S36_L004_R2_001.fastq.gz \
EPI-230_S37_L004_R1_001.fastq.gz \
EPI-230_S37_L004_R2_001.fastq.gz \
EPI-41_S38_L005_R1_001.fastq.gz \
EPI-41_S38_L005_R2_001.fastq.gz \
EPI-42_S39_L005_R1_001.fastq.gz \
EPI-42_S39_L005_R2_001.fastq.gz \
EPI-43_S40_L005_R1_001.fastq.gz \
EPI-43_S40_L005_R2_001.fastq.gz \
EPI-44_S41_L005_R1_001.fastq.gz \
EPI-44_S41_L005_R2_001.fastq.gz \
> /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_trimgalore.stdout.log \
2> /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_trimgalore.stderr.log
sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 2476m19.582s user 4465m5.380s sys 161m8.248s
%%bash
cd /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/
time \
for fq in *_val*.gz
do md5sum "$fq" >> checksums.md5
done
tail /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/checksums.md5
sed '/^Subject:/ s/ / checksums JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
85ec9e3b29b275ee66ec3be160bad40c EPI-230_S37_L004_R1_001_val_1.fq.gz 19d0bd60270191591904eb0b3a1f5ccc EPI-230_S37_L004_R2_001_val_2.fq.gz 449084831e4c9ca324d7e956fcd00d55 EPI-41_S38_L005_R1_001_val_1.fq.gz 451ce4da5f41a1fb7a5391d24eb2230a EPI-41_S38_L005_R2_001_val_2.fq.gz 5e1780aff85d128b13f4ed2527a068da EPI-42_S39_L005_R1_001_val_1.fq.gz 5172dc0022030e5e24c2e713d6a21531 EPI-42_S39_L005_R2_001_val_2.fq.gz d06640779f9ce376084f82cbf2c15a2c EPI-43_S40_L005_R1_001_val_1.fq.gz d137cbaa90b95334b459e7a6e5e93065 EPI-43_S40_L005_R2_001_val_2.fq.gz 67ce2af15035316ba66b86965d6987e8 EPI-44_S41_L005_R1_001_val_1.fq.gz 81a9286c4fa9b4cbba42ace1118e4dca EPI-44_S41_L005_R2_001_val_2.fq.gz
real 12m26.097s user 4m53.484s sys 0m49.024s
%%bash
cd /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc
/home/shared/anaconda3/bin/multiqc .
mv /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_report.html \
/home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_data/
ls -l /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_data/
Searching 208 files.. total 3820 -rw-rw-r-- 1 sam sam 127519 May 18 08:34 mqc_fastqc_per_base_n_content_plot_1.txt -rw-rw-r-- 1 sam sam 122609 May 18 08:34 mqc_fastqc_per_base_sequence_quality_plot_1.txt -rw-rw-r-- 1 sam sam 83123 May 18 08:34 mqc_fastqc_per_sequence_gc_content_plot_Counts.txt -rw-rw-r-- 1 sam sam 216075 May 18 08:34 mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt -rw-rw-r-- 1 sam sam 41835 May 18 08:34 mqc_fastqc_per_sequence_quality_scores_plot_1.txt -rw-rw-r-- 1 sam sam 117874 May 18 08:34 mqc_fastqc_sequence_duplication_levels_plot_1.txt -rw-rw-r-- 1 sam sam 53330 May 18 08:34 mqc_fastqc_sequence_length_distribution_plot_1.txt -rw-rw-r-- 1 sam sam 215878 May 18 08:34 multiqc_data.json -rw-rw-r-- 1 sam sam 24211 May 18 08:34 multiqc_fastqc.txt -rw-rw-r-- 1 sam sam 10632 May 18 08:34 multiqc_general_stats.txt -rw-rw-r-- 1 sam sam 30727 May 18 08:34 multiqc.log -rw-rw-r-- 1 sam sam 2822352 May 18 08:34 multiqc_report.html -rw-rw-r-- 1 sam sam 19018 May 18 08:34 multiqc_sources.txt
[INFO ] multiqc : This is MultiQC v1.5.dev0 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching '.' [INFO ] fastqc : Found 104 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete
%%bash
find /mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/ \
-type d
/mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/ /mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc /mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_data
%%bash
cd /mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/
time \
md5sum -c checksums.md5
sed '/^Subject:/ s/ / checksums JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
EPI-103_S27_L005_R1_001_val_1.fq.gz: OK EPI-103_S27_L005_R2_001_val_2.fq.gz: OK EPI-104_S28_L005_R1_001_val_1.fq.gz: OK EPI-104_S28_L005_R2_001_val_2.fq.gz: OK EPI-111_S29_L005_R1_001_val_1.fq.gz: OK EPI-111_S29_L005_R2_001_val_2.fq.gz: OK EPI-113_S30_L005_R1_001_val_1.fq.gz: OK EPI-113_S30_L005_R2_001_val_2.fq.gz: OK EPI-119_S31_L005_R1_001_val_1.fq.gz: OK EPI-119_S31_L005_R2_001_val_2.fq.gz: OK EPI-120_S32_L005_R1_001_val_1.fq.gz: OK EPI-120_S32_L005_R2_001_val_2.fq.gz: OK EPI-127_S33_L005_R1_001_val_1.fq.gz: OK EPI-127_S33_L005_R2_001_val_2.fq.gz: OK EPI-128_S34_L005_R1_001_val_1.fq.gz: OK EPI-128_S34_L005_R2_001_val_2.fq.gz: OK EPI-135_S35_L005_R1_001_val_1.fq.gz: OK EPI-135_S35_L005_R2_001_val_2.fq.gz: OK EPI-136_S36_L005_R1_001_val_1.fq.gz: OK EPI-136_S36_L005_R2_001_val_2.fq.gz: OK EPI-143_S37_L005_R1_001_val_1.fq.gz: OK EPI-143_S37_L005_R2_001_val_2.fq.gz: OK EPI-145_S38_L005_R1_001_val_1.fq.gz: OK EPI-145_S38_L005_R2_001_val_2.fq.gz: OK EPI-151_S2_L002_R1_001_val_1.fq.gz: OK EPI-151_S2_L002_R2_001_val_2.fq.gz: OK EPI-152_S3_L002_R1_001_val_1.fq.gz: OK EPI-152_S3_L002_R2_001_val_2.fq.gz: OK EPI-153_S4_L002_R1_001_val_1.fq.gz: OK EPI-153_S4_L002_R2_001_val_2.fq.gz: OK EPI-154_S5_L002_R1_001_val_1.fq.gz: OK EPI-154_S5_L002_R2_001_val_2.fq.gz: OK EPI-159_S6_L002_R1_001_val_1.fq.gz: OK EPI-159_S6_L002_R2_001_val_2.fq.gz: OK EPI-160_S7_L002_R1_001_val_1.fq.gz: OK EPI-160_S7_L002_R2_001_val_2.fq.gz: OK EPI-161_S8_L002_R1_001_val_1.fq.gz: OK EPI-161_S8_L002_R2_001_val_2.fq.gz: OK EPI-162_S9_L002_R1_001_val_1.fq.gz: OK EPI-162_S9_L002_R2_001_val_2.fq.gz: OK EPI-167_S10_L002_R1_001_val_1.fq.gz: OK EPI-167_S10_L002_R2_001_val_2.fq.gz: OK EPI-168_S11_L002_R1_001_val_1.fq.gz: OK EPI-168_S11_L002_R2_001_val_2.fq.gz: OK EPI-169_S12_L002_R1_001_val_1.fq.gz: OK EPI-169_S12_L002_R2_001_val_2.fq.gz: OK EPI-170_S13_L002_R1_001_val_1.fq.gz: OK EPI-170_S13_L002_R2_001_val_2.fq.gz: OK EPI-175_S14_L003_R1_001_val_1.fq.gz: OK EPI-175_S14_L003_R2_001_val_2.fq.gz: OK EPI-176_S15_L003_R1_001_val_1.fq.gz: OK EPI-176_S15_L003_R2_001_val_2.fq.gz: OK EPI-181_S16_L003_R1_001_val_1.fq.gz: OK EPI-181_S16_L003_R2_001_val_2.fq.gz: OK EPI-182_S17_L003_R1_001_val_1.fq.gz: OK EPI-182_S17_L003_R2_001_val_2.fq.gz: OK EPI-184_S18_L003_R1_001_val_1.fq.gz: OK EPI-184_S18_L003_R2_001_val_2.fq.gz: OK EPI-185_S19_L003_R1_001_val_1.fq.gz: OK EPI-185_S19_L003_R2_001_val_2.fq.gz: OK EPI-187_S20_L003_R1_001_val_1.fq.gz: OK EPI-187_S20_L003_R2_001_val_2.fq.gz: OK EPI-188_S21_L003_R1_001_val_1.fq.gz: OK EPI-188_S21_L003_R2_001_val_2.fq.gz: OK EPI-193_S22_L003_R1_001_val_1.fq.gz: OK EPI-193_S22_L003_R2_001_val_2.fq.gz: OK EPI-194_S23_L003_R1_001_val_1.fq.gz: OK EPI-194_S23_L003_R2_001_val_2.fq.gz: OK EPI-199_S24_L003_R1_001_val_1.fq.gz: OK EPI-199_S24_L003_R2_001_val_2.fq.gz: OK EPI-200_S25_L003_R1_001_val_1.fq.gz: OK EPI-200_S25_L003_R2_001_val_2.fq.gz: OK EPI-205_S26_L004_R1_001_val_1.fq.gz: OK EPI-205_S26_L004_R2_001_val_2.fq.gz: OK EPI-206_S27_L004_R1_001_val_1.fq.gz: OK EPI-206_S27_L004_R2_001_val_2.fq.gz: OK EPI-208_S28_L004_R1_001_val_1.fq.gz: OK EPI-208_S28_L004_R2_001_val_2.fq.gz: OK EPI-209_S29_L004_R1_001_val_1.fq.gz: OK EPI-209_S29_L004_R2_001_val_2.fq.gz: OK EPI-214_S30_L004_R1_001_val_1.fq.gz: OK EPI-214_S30_L004_R2_001_val_2.fq.gz: OK EPI-215_S31_L004_R1_001_val_1.fq.gz: OK EPI-215_S31_L004_R2_001_val_2.fq.gz: OK EPI-220_S32_L004_R1_001_val_1.fq.gz: OK EPI-220_S32_L004_R2_001_val_2.fq.gz: OK EPI-221_S33_L004_R1_001_val_1.fq.gz: OK EPI-221_S33_L004_R2_001_val_2.fq.gz: OK EPI-226_S34_L004_R1_001_val_1.fq.gz: OK EPI-226_S34_L004_R2_001_val_2.fq.gz: OK EPI-227_S35_L004_R1_001_val_1.fq.gz: OK EPI-227_S35_L004_R2_001_val_2.fq.gz: OK EPI-229_S36_L004_R1_001_val_1.fq.gz: OK EPI-229_S36_L004_R2_001_val_2.fq.gz: OK EPI-230_S37_L004_R1_001_val_1.fq.gz: OK EPI-230_S37_L004_R2_001_val_2.fq.gz: OK EPI-41_S38_L005_R1_001_val_1.fq.gz: OK EPI-41_S38_L005_R2_001_val_2.fq.gz: OK EPI-42_S39_L005_R1_001_val_1.fq.gz: OK EPI-42_S39_L005_R2_001_val_2.fq.gz: OK EPI-43_S40_L005_R1_001_val_1.fq.gz: OK EPI-43_S40_L005_R2_001_val_2.fq.gz: OK EPI-44_S41_L005_R1_001_val_1.fq.gz: OK EPI-44_S41_L005_R2_001_val_2.fq.gz: OK
real 21m33.769s user 4m45.188s sys 0m32.968s