-----------------------
Start of variable list:
-----------------------
Sample_ID:
A8-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 19:49:49 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791359
Current job name : Step_02_A8-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/8791359.1.linga

Loading required modules...


List files in scratch directory:

total 38M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 A8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:49 SRR6575593_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:49 SRR6575593_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575593_1.fastq <==
@SRR6575593.1 1/1
TTCCTATATAGCCGAAAGGTTCTTTTTTTCCGGAGTAGTAAGTAACTACATGTGAAATAATTCCAAATCCTGGGAGGATAAGAATATAAACTTCTGGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575593.2 2/1
GTATTGCGCTTGATGAGGACAGTCATGACTCCGCCAGCAGTTTCAATACCAAGGGAAAGAGGAGTGACATCCAAGAGCAGCAAATCCTGAACGTTCTCAG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575593.3 3/1
AAACTAGGCTCTGAGACGCCAATGGACAGGCCTCTGTGAGAGTCCGGGAGAACATGCGGAAGAGGGACCAGTCTTTCTTCCCCTGTCCTGTGATGAAGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575593.4 4/1
CTTCAGACACGGGGCCGCTGTGGCGGCAGCAGAAAGCACCACCCGGGACAGCATTGTCTGCGAAGAGCGGGACAGCGGGCTCCGTGTCCCTGTGACCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575593.5 5/1
ACAAGATCCAGGATGAGGCGGGACTATAGACAGAGTGAAGATCAAGAGTGGTGGCCACTCCTGTGAGCTTAGGAAGGGGCCACCTGTCCCAAGAAGCCTG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575593_2.fastq <==
@SRR6575593.1 1/2
CCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCAGAAGTTTATATTCTTATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575593.2 2/2
GTCTTGGTGGGTGGTTCTACCAGAATCCCCAAGATTCAGAAACTTCTGCAAGACTTCTTCAATGGAAAAGAGCTGAACAAGAGCATTAACCCCGATGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6575593.3 3/2
ACGCAGAGTACATGGGGAAGCGGCCGCAGGTATGGCGGCTGCCATGCCGATCGGTTTGCCGTTGCGGTAACTGGTGCTGTTGCTGGTGGGACGGGGCTGC
+
8FFFFF-FF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFF-FFFFFFF-F-FFFF-FFFFF-FFFFFFFFFFFF-FFF-88F
@SRR6575593.4 4/2
TATCAACGCAGAGTACATGGGGACAGGCTCGGGTCGGGGTCACAGGGACACGGAGCCCGCTGTCCCGCTCTTCGCAGACAATGCTGTCCCGGGTGGTGCT
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8-FFFFFFFFFFFFFFFFFFF
@SRR6575593.5 5/2
GCATCATGCAGTCCTGCTGGGACCTGGAGCCTACCAGAAGACCCACCTTCCAACAGATCTGCTTCCTCCTCCAGGAGCAGGCCCGACTGGAGAGGAGAGA
+
FFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFF-FF

Starting FASTQC command


Processing SRR6575593_1.fastq

Printing command:
fastqc --outdir SRR6575593_1.fastq

Analysis complete for SRR6575593_1.fastq

Processing SRR6575593_2.fastq

Printing command:
fastqc --outdir SRR6575593_2.fastq

Analysis complete for SRR6575593_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 198M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 79 root   root       92K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 A8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  99M Oct 12 19:49 SRR6575593_1.fastq
-rw-r--r--   1 kkarri waxmanlab  99M Oct 12 19:49 SRR6575593_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:15 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================