-----------------------
Start of variable list:
-----------------------
Sample_ID:
N22-MAA000377-3_9_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 19:41:28 EDT 2018
Running on node : scc-yf1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790874
Current job name : Step_02_N22-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790874.1.y

Loading required modules...


List files in scratch directory:

total 38M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576891_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576891_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576891_1.fastq <==
@SRR6576891.1 1/1
GGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGCTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFF
@SRR6576891.2 2/1
CCCACCCACTCCCCTACACCCACTCCCACTTCTTGGCCTTGGTGTTCCCCGGTACTGGGGCATATAAAGTTTGCAAGACCAAGGGGCCTCTCTTCCCAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576891.3 3/1
CCATTGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTAATTGTCGATATGAACTCTTAAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576891.4 4/1
GCCAGGCAGTGATGGTGTATGCCTTTAATCCCAGCACTCAGGAGGTAGAGGCAGGTGGATCTCTGTGAGTTCCAGGTCAGCTTAGCCTACAAAGGGAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576891.5 5/1
ATCCCAAAGTGCTGGGTTATAGACGTGAGCCACCAAACCCAGCCAGCATGGACTATGTGTAAGCCAGAGGATTCCCACAGCGCTCAGCATGGGGAAATAC
+
FFFFFFFFFFFF8FFF8FF8FFFF8FFF8F8F88FFFFFFF8FF888F-FFF---FFFF-FFF-FF-F-FF--FFF-FF-FFFF-F-F-F---FF-F-FF

==> SRR6576891_2.fastq <==
@SRR6576891.1 1/2
CACCTCCCCAGTGTTGAAGTTACAAGTGTACACTATCATGCCTCACTTTCTTACATGAGCTTTGGCGAATGATCAAAATCAAGTCTCACAAGCACTTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFF--FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576891.2 2/2
GTCAGCTATTGGCTGGAACACAGGGCCCCCAATGGAGGAGCTAGAGAAAGTACCCAAGGAGCTAAAGGGATCTGCAGCCCTATAGGTGGAACAACAATAT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576891.3 3/2
GTACATGGGCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCCGAATGATTATAACCTAGACTTACAAGTCAAAGTAAAATCAACATATCTTATTGACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576891.4 4/2
GAATAGTGTCTGTGTTTTTAGGCTCTCCATCCCCCAGACATCTCAGAACTAGCCTTAGTCTTTAGTCCTCTCAACCCACAGTGAGCAGATGGAGGTGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576891.5 5/2
CAGGGAGATCATATAGATAATTCTACCCAGGTTTGAGAAGAAATCTGAAACTATTCAGTCCAGCTTTTATCCCGGACTTGGACAGGGACACACTGTCTTC
+
FFFFFFFFFFFFFFFFFFFF8F8F888FFF-8-8--FFFFFF-FFF-FFF-FFFFFFFF-FF--FFF-FFF--F-FFFF--FFFFF-FFF-FF-FFFF-F

Starting FASTQC command


Processing SRR6576891_1.fastq

Printing command:
fastqc --outdir SRR6576891_1.fastq

Analysis complete for SRR6576891_1.fastq

Processing SRR6576891_2.fastq

Printing command:
fastqc --outdir SRR6576891_2.fastq

Analysis complete for SRR6576891_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 190M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  95M Oct 12 19:41 SRR6576891_1.fastq
-rw-r--r--   1 kkarri waxmanlab  95M Oct 12 19:41 SRR6576891_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:43 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================