-----------------------
Start of variable list:
-----------------------
Sample_ID:
B14-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 19:42:21 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790963
Current job name : Step_02_B14-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/8790963.1.linga

Loading required modules...


List files in scratch directory:

total 54M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:42 SRR6576491_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:42 SRR6576491_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576491_1.fastq <==
@SRR6576491.1 1/1
TGACAAGCCTTTGACTAGAAACCTTTGTTCCTACCTCTGGCTGGAACACAGCTGGCAATATCAACAGCAGAGGTGTCTGAGTCCAGAGAAAGACTGTCCT
+
FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576491.2 2/1
TATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576491.3 3/1
GTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576491.4 4/1
GCCCACATAGCATGCAAGTTTGCTGAGCTTAAAGAAAAGATCGATCGTCGTTCTGGTAAGAAGCTGGAAGATGGCCCCAAGTTCCTGAAGTCTGGCGATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576491.5 5/1
CCCGGATGATCTGGTTGCGCACGGCCGGTTTGATCTCCAGGTGGATCAGCTTTCTGGCCATGATGAGGCCTGACGGCCTATGCCGGGCCTTGGTGACCAC
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF

==> SRR6576491_2.fastq <==
@SRR6576491.1 1/2
NGACACAGCTATTGGGGGGGGGGGTCATAGTTTGTTTCATGTGAAAAATTTTTAAAAACTGATATTCAAAGACCGAGAGACTCATGATCCAAGTTCCAGC
+
#F8FFFFF8FFF8FFFFFFFFFFFFFFFF8FFF8FFFFFFFF-FFFF-FFFFF-F-FFFF--FFFFFFF---FF-F-FFF-FFFF-FFFF8F-FFFFFFF
@SRR6576491.2 2/2
NTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576491.3 3/2
GTATCAACGCAGAGTACATGGGGAAGTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTG
+
F-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFF
@SRR6576491.4 4/2
CTGATTAAGACTGGGGTGGCAGGTGTTAGGGGTAATATTCATTTAGCCTTCTGAGCTTTCTGGGCAGACTTGGTGACTTTGCCAGCTCCAGCAGCCTTCT
+
FFFFFFFFFFF8F8FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFF8FFFF-FFFF-FFF
@SRR6576491.5 5/2
CTATCAACCCTACCATCGCCGAGGGCCCGTCCCCCACCAGCGAGGGCGCCTCTGAGGCAAACCTGGTGGACCTCCAGAAGAAGCTGGAAGAGCTGGACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F8F-FFFFFFFFF

Starting FASTQC command


Processing SRR6576491_1.fastq

Printing command:
fastqc --outdir SRR6576491_1.fastq

Analysis complete for SRR6576491_1.fastq

Processing SRR6576491_2.fastq

Printing command:
fastqc --outdir SRR6576491_2.fastq

Analysis complete for SRR6576491_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 289M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 145M Oct 12 19:42 SRR6576491_1.fastq
-rw-r--r--   1 kkarri waxmanlab 145M Oct 12 19:42 SRR6576491_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:54 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================