-----------------------
Start of variable list:
-----------------------
Sample_ID:
N8-MAA000907-3_11_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:42:17 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790879
Current job name : Step_02_N8-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790879.1.linga

Loading required modules...


List files in scratch directory:

total 25M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:42 SRR6576654_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:42 SRR6576654_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576654_1.fastq <==
@SRR6576654.1 1/1
GACTAGCAGTGATGACCATTTGTGTTCAAACAAGGGTTCTGTTGGGTTCTTGTTCTATGCTGAATTCCGCTTCCTCTGAAATCTATATATCAAATCCCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576654.2 2/1
GTACTTAGGTTATAGGCACCAAACGGGCATGGGTGGCCATTCCACGCAACCATTCTTAAGTTTCTTAATAAAGTTGGATACAAAGTCATCTGTGAAGAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576654.3 3/1
CCTTTATATTTCTAATAAGCCTTAAAAGCACTAGAGCTGAGCAGAATCTACACTCGAAGCTATTCTATTTCCCTGCCTGTGACCCTGTGATATGACTTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576654.4 4/1
TTACTATACTACTAACAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGG
+
8FFFF8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFF
@SRR6576654.5 5/1
GATGGATATATATTTATGAATACATTAAAAATCACATTTCTTTATACAATAATTAACCGGTTAAAGCAAAAGGAATAACCACCAACCAGTGTACTGTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576654_2.fastq <==
@SRR6576654.1 1/2
NCCTTAGGGTCTTTGTGTGTCCAAATCTCTTATTATAATGAGTCAGTTGAGTTTAGAGCCCATCTTCACATTCTAATTTCAAATTAATCATATCCTTAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-
@SRR6576654.2 2/2
TCTCAGAGGCTCCCATAGCAAACGTCAGAGTATTGCCGGGCTAGCCCTTGTTAGGGCCGTCTAGGAAGATCTCCAGTGGAGAAGGGTGTTACCTTCCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576654.3 3/2
GTTGATAGCTGGGTGAAAGAGAGGTAGGTGGGGTTTTGCTTTCTGGGCTTGGAGTGTGAGGCAGAACCACAAGAGGGAAGAGAGTAGGTAGAGAGAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF8
@SRR6576654.4 4/2
CATCTAATCCTACTGTGAATATGTGGTGGGCTCATACAATAAAGCCTAGAAAGCCAATAGACATTATTGCTCATACTATTCCTATATAGCCGAAAGGTTC
+
FFFFFFFFFFFFFFFFFFFFFFF8F-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFF-FF-FF-FFFF8FF--FF-FFFFF-FF
@SRR6576654.5 5/2
CGTACACACACACAACACCTCACAGTACACTGGTTGGTGGTTATTCCTTTTGCTTTAACCGGTTAATTATTGTATAAAGAAATGTGATTTTTAATGTATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576654_1.fastq

Printing command:
fastqc --outdir SRR6576654_1.fastq

Analysis complete for SRR6576654_1.fastq

Processing SRR6576654_2.fastq

Printing command:
fastqc --outdir SRR6576654_2.fastq

Analysis complete for SRR6576654_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 125M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 N8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  63M Oct 12 19:42 SRR6576654_1.fastq
-rw-r--r--   1 kkarri waxmanlab  63M Oct 12 19:42 SRR6576654_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:38 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================