-----------------------
Start of variable list:
-----------------------
Sample_ID:
L13-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 19:41:26 EDT 2018
Running on node : scc-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790703
Current job name : Step_02_L13-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/8790703.1.linga

Loading required modules...


List files in scratch directory:

total 31M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 37 root   root       20K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576591_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576591_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576591_1.fastq <==
@SRR6576591.1 1/1
GTATTTCATCAGTCATCGGGGCAGGTTTGGGCCTTGGGATCCTTTGGCTGTGGCCACTTCTCCTTATCAGATCTCGCAGGCTCATTTTCTCATATTCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576591.2 2/1
GTGAGAAAAAACTAGGCTACAGAGTTAGGATATTGCCCAGAAATCTCACTAAGTCTGTGTTTGAAAGTTGCACTTTTTACAATATCATGTAAGGGAAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576591.3 3/1
CTGCTGGTCTGGTAGCAGAACTACTCATCTTCCTACTTTGGCACAAACTGGGTAGACAGCCTCCAATCAATACACGCTTCTGTTTAGTTTGAGACTGGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576591.4 4/1
GTTATCAACGCAGAGTACATGGGGAGAGGTCCCCGGGCCTCGGAGGCGGCCAGCCCGGGCTGGGTCGCGCGATGTCTCATGGATCGGGGCTCGTCCGGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576591.5 5/1
CCCTGGAGCAGCGTGAGGGCCGATGCTCAGTTGTCCACCTCAATGTGGCCCCTCGCCCCCGGCATTCCAGAGGGGGCTCAGGGCCCGAGGCAGCTGTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576591_2.fastq <==
@SRR6576591.1 1/2
NAACAGAAGAAAAGGTAGTGGTACACCTTAAGAAGTTGGATACTGCCTACGACGAGCTGGGCAATTCCGGGCATTTTACCCTCATTTACAACCAAGGCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576591.2 2/2
ATATATATCTATCTCCATCCCTTGGAGCTGGCGCTCTAGGCAGTTGTGAGCTGACCAGCATAGCTGGGAACCAAACGTGGGCCTTCTGCACGAGTAGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576591.3 3/2
GCTTAGGGCCTGGAGATGTATATAACTCAGTTGGCAGAATTCATGCCTAGCATGCACAAAACTGGGTGCTATCCTTAGTACTGCATAAAACCCAGTATAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576591.4 4/2
GAGGTGCACCAGGTAAAAGATGAGGATCATTATCAGGTCGCACATGGTGACGACTTCGAAGAAGCTGTGGGCACCATAGTCGATCGGAACGGAGCTTCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576591.5 5/2
GCCGTGTCAAGGGCCCTAAGTGTCTGACACTCATGATGCTCCATGACTGCGCCGGGGTTGGAGATTCCGAGCGTGGCTTGCACTGCTAAGCACCGGCAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576591_1.fastq

Printing command:
fastqc --outdir SRR6576591_1.fastq

Analysis complete for SRR6576591_1.fastq

Processing SRR6576591_2.fastq

Printing command:
fastqc --outdir SRR6576591_2.fastq

Analysis complete for SRR6576591_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 159M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 39 root   root       20K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:41 SRR6576591_1.fastq
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:41 SRR6576591_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================