-----------------------
Start of variable list:
-----------------------
Sample_ID:
F18-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 19:49:50 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791373
Current job name : Step_02_F18-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/8791373.1.linga

Loading required modules...


List files in scratch directory:

total 45M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 102 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 F18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  22M Oct 12 19:49 SRR6576159_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  23M Oct 12 19:49 SRR6576159_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576159_1.fastq <==
@SRR6576159.1 1/1
GGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576159.2 2/1
CAACCATGTATGTAGAAAACCAGGCCAACCTCGGAGCCCTGAACTCCACACACCTCCACTTGAAAATGAGCCCTCTCTAAGGTCTCTGGGGTGGCTCAGC
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576159.3 3/1
GCCTTGGCTGGCTGTCCAAACACGTGGCGGAATTTGCTGGAGCGAACCACCTGCCGGCTCATCCTGCTGCGGAGAGCTGAGCGTGACCCCTCCCAAGTAG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576159.4 4/1
GTCTGAGCGCGAACCCTGCCCATTCAGGTCGGAGCACCATTGGGAGCAGGGTTCCATCCTGTGGTCAGGGGGTTGCTGTGCTCCTGAAAAAAAAAAAAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576159.5 5/1
CTGGAGACCCGGAATGCAGAGCTGGAGCAGCAGCTGCGGTCGATGGAGTGCAACCTGGAGGAGGCGCGGGCCGAGCGGGAGCGCGCACGGGCGGAGGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576159_2.fastq <==
@SRR6576159.1 1/2
GAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACT
+
FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576159.2 2/2
GGCCTGCCCCACTGCATAGTTATTGTTAGGGCTTGTCCCAAAGAATCCATGGATTGGTGGATGTGAGGGCATCACCCATCCATCTCTGGAACCTAGCCTA
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF8F
@SRR6576159.3 3/2
TGACAGAGCATCCTCGGTGGCCAGCCTGCAGCTCCTCCATCCTTCTCTCCTTCCTCCTCTACTTGGGAGGGGTCACGCTCAGCTCTCCGCAGCAGGATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576159.4 4/2
CACTTAAGCACTGGAGGCAAAGCCTCCAGCAGACTCTGCCCTGGGAGTTCGGCTGCCTGCATCTTTTTTCTCCTTTTCTTTTCTTTCTTTCTTTCTTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-F-FFFF-FF--FFFFFF---F-F--FF----8---FF-F-FFFFF
@SRR6576159.5 5/2
CAGCTGGGGTCCCCTGGCCCCTGCCAGGGCGCCTTGAGGCCGCAGACACTCCATGGCAGACTAGGGTGCTGCCTCTGCCAGGCGTGCCAGGCCTTCACGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF

Starting FASTQC command


Processing SRR6576159_1.fastq

Printing command:
fastqc --outdir SRR6576159_1.fastq

Analysis complete for SRR6576159_1.fastq

Processing SRR6576159_2.fastq

Printing command:
fastqc --outdir SRR6576159_2.fastq

Analysis complete for SRR6576159_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 230M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 F18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 115M Oct 12 19:49 SRR6576159_1.fastq
-rw-r--r--    1 kkarri waxmanlab 115M Oct 12 19:49 SRR6576159_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:17 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================