-----------------------
Start of variable list:
-----------------------
Sample_ID:
D1-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 19:44:29 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791062
Current job name : Step_02_D1-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/8791062.1.linga

Loading required modules...


List files in scratch directory:

total 17M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 8.3M Oct 12 19:44 SRR6576221_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab 7.8M Oct 12 19:44 SRR6576221_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576221_1.fastq <==
@SRR6576221.1 1/1
GTATCAACGCAGAGTACATGGGACTCCAGCAGATGTCTGGCTGTGACTTGGGGTCGGACTGGCGCCTCCTCCGCGGGTACCTGCAGTTCGCCTATGAAGG
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF--FFFFFFFFF-FF
@SRR6576221.2 2/1
TCCCAGAGTTAAGGCACCTGGCACGGAGTGGCTGCAGAGCTACCAGAGTGAGTGTCCCTTCCTCCTCAGGCCCTTCCTCAAGCACGGCAGGGCTGCAGAA
+
FFFFFFFFF-FF-FFFFFF8FFFFFFFFF8FF8FFFFFFFF-FFFFFF-FFF-FFFFFF-FFFFFFF-FFFFFFFFFFF-FFFFFF-FFFF-FFFFFFFF
@SRR6576221.3 3/1
TTATAGAAGCCATTACATTATATCACCCCCATTTTCCACACTATTTTCACCCATCCTGTTATTTTCTTTCAATAAATCAGTCTTCCACATAACTCAAACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576221.4 4/1
CTTCATCAGAAGAGTACACACCCAAGAATATAGGATATATAAATAGTATGAAGTAGACTTTGTTCTAGGGAAGGAGTCAAGTATTGGCAAGAGTTTGGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFF-FF-FF
@SRR6576221.5 5/1
TCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACAG
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6576221_2.fastq <==
@SRR6576221.1 1/2
CCTCAGGGTGACTTCACCTTTAGATCTGGGGTGATGGGTCACATGTGCCTTTGGGGAATCTGTGCGCAGCAGCGTCGCGTTCCCGTTCTTCAGGTATCTG
+
FFFFFFFFFFFFFFFFFFF88FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8FFF
@SRR6576221.2 2/2
CTACCCACCAGCCATTGTGCAGCCCAGCGTGGTGATCCCTGCCACCCCTGTCCCGTCACTGTCCTCGCCCTACCTTGAGTATACACCAGCCAGCCCAGCC
+
FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FF-F--FFFFFFFFFFFFFFFFF---FFF8-FFFFFFFFFF8FFFFFFFF
@SRR6576221.3 3/2
GATATATGGAGATGATGGTACTTAAAAAGGACGTTTTTTCAAAGATTGGCTTGTGGTGTGAGAAGCAGCCACAGAAGTGGCAGATGCCATTCTTGTGGAT
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-8FFFFFFFF
@SRR6576221.4 4/2
CACACACACACACACACACAATCACATACAGAGACACAAATTTCAATTATTAATAAAAGACAATATATCTTTCAATATGGCTATTATCAAATACTCTGGT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FF-FFFFFFFF8F
@SRR6576221.5 5/2
GCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF

Starting FASTQC command


Processing SRR6576221_1.fastq

Printing command:
fastqc --outdir SRR6576221_1.fastq

Analysis complete for SRR6576221_1.fastq

Processing SRR6576221_2.fastq

Printing command:
fastqc --outdir SRR6576221_2.fastq

Analysis complete for SRR6576221_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 80M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  40M Oct 12 19:44 SRR6576221_1.fastq
-rw-r--r--    1 kkarri waxmanlab  40M Oct 12 19:44 SRR6576221_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:52 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================