-----------------------
Start of variable list:
-----------------------
Sample_ID:
O22-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 19:49:49 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791354
Current job name : Step_02_O22-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/8791354.1.linga

Loading required modules...


List files in scratch directory:

total 46M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 36 root   root      116K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 O22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:49 SRR6575215_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:49 SRR6575215_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575215_1.fastq <==
@SRR6575215.1 1/1
GACCAGATCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGAACAGATACCGTCGTAGTTCCGACCATAAAC
+
8FF-FFF-FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6575215.2 2/1
GTCACTTAGAGAGCTGAGACACTACAGCAAGTGAAGGCTTGCACCTTTCACTTGCCCAGAGGAAGCTCTGACGAAGGGGGTGCATCAACCAGCTCCTGTG
+
F-F-FFFFFFFFFFFFFFFFF8FFFF8FFF8F8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF--FF-FF-FFF-FFFFF-FFFFFFFFF-FFF-
@SRR6575215.3 3/1
GCAAGGGCCACCAGAGGGCCAGAGAGGTGCTTGAGACAGGGCCACCTGGCTGGATATGGATGTTGTTGCAGGACAGGAGAAGGATACTCATTGATTCTCC
+
FF8FFFFFFFFFFFFFFFFF8FFFFFF8FF8FF8FFFFFFFFF-F8FFFFFFFFF-FFF-FF-FFFFFF-FFFFFFFFFF-FFF-FFFFFFFFFFFFFF-
@SRR6575215.4 4/1
TCCTTAGTCTGGCTGTCATGTGACAGTGGTCCGCCATCTCAGTTGCCAGACCCTGTGCACTAGTCAGTCTCCACTGTGTGGGAGGTTCTTGTTTTATCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF
@SRR6575215.5 5/1
ACCTACCTCTCTCTGGGCTTCTTTTTTGATCGGGATGACGTGGCTCTGGAGGGCGTAGGCCACTTCTTCCGCGAATTGGCCGAGGAGAAGCGCGAGGGCG
+
FFFFFF-FFFFFFFFFFFFFFFFFFF88FFFFFFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF--FFFFFFFFF

==> SRR6575215_2.fastq <==
@SRR6575215.1 1/2
NCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF8FF
@SRR6575215.2 2/2
NACCCTGACTTCTCAAATATGAGGTGGCGGCAGTGACAGCAGCAGCTGCTGGGGGCTGCCTCGGACTCCTTAGACAACTTACACAGGAGCTGGTTGATGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575215.3 3/2
CCTGCGCAAGATGCGCAAGCGCTTGATGCGGGATGCCGAGGATCTGCAGAAGCGCCTCGCTGTGTACAAGGCAGGGGCACGCGTGGGCGCCGAGCGCGGT
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFF-FF-FFFFFFFFF-FFFF-FFFFFFFF-8FF88F8
@SRR6575215.4 4/2
CACACACACACACACAAAATCACCTGTGCCTCTGAGAAGTGCCAGGTGTGGCCAAGGTCTACCTCTGGACCAGCAAGTACTGTGACTGTAAGCCAGCCCT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF--
@SRR6575215.5 5/2
GAGCAGAGGGGGGAGCCCCTTGGAAGGTACAGAGGCCTCCTAGTCGTGCTTGAGAGTGAGGCGCTCAAAGAGATACTCGCCCAGAGACCCCTGGGGCGCG
+
FFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575215_1.fastq

Printing command:
fastqc --outdir SRR6575215_1.fastq

Analysis complete for SRR6575215_1.fastq

Processing SRR6575215_2.fastq

Printing command:
fastqc --outdir SRR6575215_2.fastq

Analysis complete for SRR6575215_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 233M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 36 root   root      116K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 O22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 117M Oct 12 19:49 SRR6575215_1.fastq
-rw-r--r--   1 kkarri waxmanlab 117M Oct 12 19:49 SRR6575215_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:07 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================