-----------------------
Start of variable list:
-----------------------
Sample_ID:
D5-MAA100039-3_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 19:44:30 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791081
Current job name : Step_02_D5-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791081.1.linga

Loading required modules...


List files in scratch directory:

total 95M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D5-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:44 SRR6576874_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:44 SRR6576874_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576874_1.fastq <==
@SRR6576874.1 1/1
CTGCTAGGGCGTGGCTCACTTTCTGGCCAATCAGCTCATCTGATTCTCCAAAGACATGTCTTCTTTCTGAGTGCCCCAGCACGACCCAGGTGGCTCCTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576874.2 2/1
TCCATGATCAGACCAAGCCAGACTCCAACAGATAAGAAAAACAAAACCACTTCCCCAAAATTAAAGCTACCAGTAAGATCCCCAAACCTCAAACCAAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576874.3 3/1
CGGCAGTCGAGTACATGCACCAGCTACAGTGCTAGACAGCCAGTTTAGGCGTAGCACTCGCTGTTATAGCCGAGCACACTCCGTAGAGAGCAGCAGCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576874.4 4/1
GAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTC
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576874.5 5/1
CTATTATCCTGGCCTCTGACAAGAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576874_2.fastq <==
@SRR6576874.1 1/2
NTACATGGGGTTTGTACTGACCTTCAGAGACTTGAGCCTGGTACAATGGCGCCTACCAGGAAGTTCTTCGTTGGGGGCAACTGGAAGATGAACGGGAGGA
+
#F-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576874.2 2/2
NGTTCAAGAAGCTCATTGGATTTTTGGTCCAGCCTTCCTTTGAGTCTTCACATGTGCTCTGTGGGGTTATTGCTGGGCTGGAGTCGGAGTTTATGGAGAC
+
#FFFFFF-FFFFFFFFFFFFF8-8FF-FF-FF-F-FFFFFFFFFFFFFFFF-FFFF-FFFF-FFF-F-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576874.3 3/2
CGTTGCAGTCTCTGTGACCTGATCGACGCGCATGTGAGCCTATAGACAGCGATGTGAGCACTCTCATCTGCGGATCAGTCTATCCTCTCTGATGCTCAGT
+
FFFFF-FFFFFF8FFFFFFF88FFF-F-FFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFF
@SRR6576874.4 4/2
ATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576874.5 5/2
GTTATCATAGTCTGTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576874_1.fastq

Printing command:
fastqc --outdir SRR6576874_1.fastq

Analysis complete for SRR6576874_1.fastq

Processing SRR6576874_2.fastq

Printing command:
fastqc --outdir SRR6576874_2.fastq

Analysis complete for SRR6576874_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 581M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D5-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 291M Oct 12 19:44 SRR6576874_1.fastq
-rw-r--r--   1 kkarri waxmanlab 291M Oct 12 19:44 SRR6576874_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:26 EDT 2018
0 hours, 0 minutes and 56 seconds elapsed.
==========================================================