-----------------------
Start of variable list:
-----------------------
Sample_ID:
J9-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 19:41:29 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790828
Current job name : Step_02_J9-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/8790828.1.linga

Loading required modules...


List files in scratch directory:

total 36M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 J9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576476_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576476_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576476_1.fastq <==
@SRR6576476.1 1/1
GGGCAAGCAGCACGGGGACGTGGTGTCCGCCATCAAGGGTGGAGGTGATGAGGCCAAGCTGCTGGTGGTAGACAAGGAAACAGATGAGTTCTTCAAGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576476.2 2/1
GATGTGCAGGCGATCGGACAGCAGGCCACACAGCAGCTTACTGTAGTTGCGGTTCTGGGCACCACCGATCTTGCCGATGCTGTGCAGGCTGCAGAGGGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576476.3 3/1
CTCTTATTACTCTGGGGCTATGATCCCGAGAGCCAAAAAGAAAAAATCAAAATAACAACAACAAGAAAAAAACAAAAAACGGCAGGGTTAGGAGATACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576476.4 4/1
CTTGTACACACTTCGACAATTATTGTAAGCACAGAATTTGCTCTATTTTTTGTTTAGTATTTAAACATGAATATTGGACCAGTTTTCTTCCTTCTTGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFF-F-FFFF-FF
@SRR6576476.5 5/1
TCACTAGACCCGAGCCGCAGGCCCTCCCGAGCTCGGTCATCCGTGCCCCGCTCCCAGATCTTTATCCGTTTGGGACCATGCGTGGAGGCGGCGTTGGGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FF-F-FFF---FFFFF-FFFFFFFFFFFFFFFFFFFFFFF--FFFFFF

==> SRR6576476_2.fastq <==
@SRR6576476.1 1/2
NTCTTTAGCCACAGCCAAGGAGATGTTGAGGTCCAAGATGGGGTCAGAGGAGGAGGAGGAGGTAGATGAGGGCTCTGTGGAAACTTGTCTCTTGGGGCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576476.2 2/2
NACCATGCCTATGTTCATCGTGAACACCAATGTTCCCCGCGCCTCCGTGCCAGAGGGGTTTCTGTCGGAGCTCACCCAGCAGCTGGCGCAGGCCACCGGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576476.3 3/2
CCCCAGAGGACTCTTGGAGGGAGCTCCAGAGCGTAGATTTGTAAAAGGGTTCTAAGCTGGAGCGCCTGAGATGCGTCCTCCTGTCATTTCTGCAAAACCA
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576476.4 4/2
GTTCCTGGTTTGTAAGTTCAAGTACAGTAGAAACTGTCTGCAGTAGGGCTATGCCTGGATAAAGAAGACGGAAGACAATGGAAAGGAGCAAGCTGGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576476.5 5/2
GCTGCACCTGCTGCGCAAGCTCTCTGGTAGGAGCCAGCACTAGACAAATTGGACCATCTCCTCTTTCCAAGTATGGCTGGTGGTTTATATGAACAATCGC
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6576476_1.fastq

Printing command:
fastqc --outdir SRR6576476_1.fastq

Analysis complete for SRR6576476_1.fastq

Processing SRR6576476_2.fastq

Printing command:
fastqc --outdir SRR6576476_2.fastq

Analysis complete for SRR6576476_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 185M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 J9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  93M Oct 12 19:41 SRR6576476_1.fastq
-rw-r--r--   1 kkarri waxmanlab  93M Oct 12 19:41 SRR6576476_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:55 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================