-----------------------
Start of variable list:
-----------------------
Sample_ID:
F3-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 19:41:28 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790780
Current job name : Step_02_F3-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/8790780.1.linga

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576312_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576312_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576312_1.fastq <==
@SRR6576312.1 1/1
CCTTTGCACCTGTGTTTGGGACCACGTAGTAAAACCCCCCTCGGTGATGGAGAGAAGGGAGTTGAGCAGCTTCTGTTGTGATTCTCAAACTGCGTTGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576312.2 2/1
GTAATACATGGTAAAGGTCTCAGCTGACAATTCTCCATACCCCATGCATGTCCCTCCAGGAAGCGCCAAAAAGTTGGTGCCAAAAAGTGCCAGAGAGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576312.3 3/1
GGCATGTACAGCTCCTTCCTGCTGTGAACTTCCCTCATAGGACAAATCAGCTTCTTTCAGTGATAACACTGACGTTTCTGTTACAGTGCCTGGACACAGT
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576312.4 4/1
CTCCATAGTGACTTACTGAGCTAGGCTCCAGCGCCGAAATGTCCTGCAGCCTCCAAACGTAGGACCAGACAGGAAACCCATGCTCAAAGGTAAGCAAGTG
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576312.5 5/1
GATTGTAGCCCAGGATGAGTCCCTCAGCGTGACGCAGTAAACTAGTAGCATCCCGATCTTTTCCCTATCTAATTCACCTCCTATTAGGAGCCGATCGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

==> SRR6576312_2.fastq <==
@SRR6576312.1 1/2
GCAAAATACAACGCAGTTTGAGAATCACAACAGAAGCTGCTCAACTCCCTTCTCTCCATCACCGAGGGGGGTTTTACTACGTGGTCCCAAACACAGGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576312.2 2/2
GTGCATCTTAAACAGGCTCTAGTGGGGTCCACTGACATCTTTGACAAGTAGCTAAGTGACAGACAGGGAGGCAAACTGCCCCTGAAGTCAAAGGACAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576312.3 3/2
CAATAGTGTCAGTTTTTAAGTCCCAACTGGCCTCAAGGTATGTTAAAAACTCTGGCTCTGAGATCCAGCATAAGTTCCAGTCTCAGAATGTAAGACACAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576312.4 4/2
CCATCTTTGGGTGACTGGTAGAGAAAGCCTAAATAAAATCAATATTAAGAATTGCCAGCTGGGGGGTCCTGGAAGCTGGTTCTGTAGTTAAAGAGCAAAC
+
8FFFF-FFFF8FFFFF8FFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-F8FF
@SRR6576312.5 5/2
CTACACATGCTAGCCGCTGGGGAGATTAGCTCGAGTTGCCCCTTTGCCCGATCCCGGAAGATACGCTCTAAGCTCGGCAATCGCTCTTGCCGTGCGAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576312_1.fastq

Printing command:
fastqc --outdir SRR6576312_1.fastq

Analysis complete for SRR6576312_1.fastq

Processing SRR6576312_2.fastq

Printing command:
fastqc --outdir SRR6576312_2.fastq

Analysis complete for SRR6576312_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 134M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:41 SRR6576312_1.fastq
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:41 SRR6576312_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:55 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================