Notebook

In [1]:

%%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 12:28:08 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:               1596.000
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        376M        295M        306M         46G         45G
Swap:           47G        281M         47G

No LSB modules are available.

In [2]:

%%bash
mkdir /home/sam/analyses/20180516_geoduck_EPI_fastqc
cd /home/sam/data/geoduck_EPI

time \
/home/shared/fastqc_v0.11.7/fastqc \
--outdir /home/sam/analyses/20180516_geoduck_EPI_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-135WG_S42_L005_R1_001.fastq.gz \
EPI-135WG_S42_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/analyses/20180516_geoduck_EPI_fastqc/20180516_geo_fastqc.out \
2> /home/sam/analyses/20180516_geoduck_EPI_fastqc/20180516_geo_fastqc.err

sed '/^Subject:/ s/ / fastqc JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"

real	119m10.036s
user	604m40.564s
sys	14m19.368s

In [3]:

%%bash
echo "Check stdout"
tail /home/sam/analyses/20180516_geoduck_EPI_fastqc/20180516_geo_fastqc.out

echo "--------------------------"
echo ""
echo "Check stderr"
tail /home/sam/analyses/20180516_geoduck_EPI_fastqc/20180516_geo_fastqc.err

Check stdout
Analysis complete for EPI-230_S37_L004_R1_001.fastq.gz
Analysis complete for EPI-230_S37_L004_R2_001.fastq.gz
Analysis complete for EPI-42_S39_L005_R1_001.fastq.gz
Analysis complete for EPI-43_S40_L005_R1_001.fastq.gz
Analysis complete for EPI-42_S39_L005_R2_001.fastq.gz
Analysis complete for EPI-43_S40_L005_R2_001.fastq.gz
Analysis complete for EPI-135WG_S42_L005_R1_001.fastq.gz
Analysis complete for EPI-135WG_S42_L005_R2_001.fastq.gz
Analysis complete for EPI-44_S41_L005_R1_001.fastq.gz
Analysis complete for EPI-44_S41_L005_R2_001.fastq.gz
--------------------------

Check stderr
Approx 80% complete for EPI-44_S41_L005_R1_001.fastq.gz
Approx 70% complete for EPI-44_S41_L005_R2_001.fastq.gz
Approx 85% complete for EPI-44_S41_L005_R1_001.fastq.gz
Approx 75% complete for EPI-44_S41_L005_R2_001.fastq.gz
Approx 90% complete for EPI-44_S41_L005_R1_001.fastq.gz
Approx 80% complete for EPI-44_S41_L005_R2_001.fastq.gz
Approx 95% complete for EPI-44_S41_L005_R1_001.fastq.gz
Approx 85% complete for EPI-44_S41_L005_R2_001.fastq.gz
Approx 90% complete for EPI-44_S41_L005_R2_001.fastq.gz
Approx 95% complete for EPI-44_S41_L005_R2_001.fastq.gz

In [4]:

%%bash
cd /home/sam/analyses/20180516_geoduck_EPI_fastqc

/home/shared/anaconda3/bin/multiqc .

mv /home/sam/analyses/20180516_geoduck_EPI_fastqc/multiqc_report.html \
/home/sam/analyses/20180516_geoduck_EPI_fastqc/multiqc_data

Searching 214 files..

[INFO   ]         multiqc : This is MultiQC v1.5.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '.'
[INFO   ]          fastqc : Found 106 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

In [5]:

%%bash
ls /home/sam/analyses/20180516_geoduck_EPI_fastqc/multiqc_data

mqc_fastqc_adapter_content_plot_1.txt
mqc_fastqc_overrepresented_sequencesi_plot_1.txt
mqc_fastqc_per_base_n_content_plot_1.txt
mqc_fastqc_per_base_sequence_quality_plot_1.txt
mqc_fastqc_per_sequence_gc_content_plot_Counts.txt
mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt
mqc_fastqc_per_sequence_quality_scores_plot_1.txt
mqc_fastqc_sequence_duplication_levels_plot_1.txt
multiqc_data.json
multiqc_fastqc.txt
multiqc_general_stats.txt
multiqc.log
multiqc_report.html
multiqc_sources.txt

In [6]:

%%bash
ls /mnt/owl/Athaliana/20180516_geoduck_EPI_fastqc/multiqc_data/

mqc_fastqc_adapter_content_plot_1.txt
mqc_fastqc_overrepresented_sequencesi_plot_1.txt
mqc_fastqc_per_base_n_content_plot_1.txt
mqc_fastqc_per_base_sequence_quality_plot_1.txt
mqc_fastqc_per_sequence_gc_content_plot_Counts.txt
mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt
mqc_fastqc_per_sequence_quality_scores_plot_1.txt
mqc_fastqc_sequence_duplication_levels_plot_1.txt
multiqc_data.json
multiqc_fastqc.txt
multiqc_general_stats.txt
multiqc.log
multiqc_report.html
multiqc_sources.txt

In [ ]: