-----------------------
Start of variable list:
-----------------------
Sample_ID:
C13-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 19:41:26 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790736
Current job name : Step_02_C13-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/8790736.1.linga

Loading required modules...


List files in scratch directory:

total 18M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 8.4M Oct 12 19:41 SRR6576713_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.0M Oct 12 19:41 SRR6576713_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576713_1.fastq <==
@SRR6576713.1 1/1
GTGTGGATATGTGCACAAGCGTAGGTACTGGCAGAAGCCAGAGGTGTCAGATCTCCCTAGACTTGGGGTCCCAGGTTGTTGTTGAGTCACCTGAAGTGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576713.2 2/1
CATATAAATAATGAAATAATGAAAATCCCTTGTTAGGATATAGCCTGTTTTTCATTATTGTCAATTTAAAAACACTTACCAAATATCTATACCCATCTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576713.3 3/1
ACACGAACGTGCGTTCAACGTGACGGGCGAGAGGGCGGCCCCCTTTCCGGCCGCACCCCGTTTCCCAAGACGAACGTCTCTCCGCTCCGGACCCCGGTCC
+
-FFFF8FFFF8FFFFFFF8FFFF8FFFFFFF8F8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFF---FF-F-F--F-FFFFFFFFF-FFF-FFFFFFFF-
@SRR6576713.4 4/1
CCCTGGGAAGGAATATGGCCCTGCCAATGCCTCCCATTCAACACTGTGATACTGATTTTAGCCTCAGGGCTTCCAGAACCATGGGAGAATAATTTATTTT
+
FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576713.5 5/1
TCCTAGATGTGACTGAGAACAAAGGTATTGCCAAAGAAGTTCTTACTCAGAGATTGGGACCCTGAAAAAGACCTGTGGCATACTTGTAAGAAATTAGACC
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576713_2.fastq <==
@SRR6576713.1 1/2
GTCCAGCACAGCCTGTGGGACGCGGCGTTCTGCTCCTTGCTCTTCGTTGTTGGGATTGAGTCCGTTTTGGAGAGTCTCCGCGGCAGCCGTCACCATCTCG
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8FFF-FF
@SRR6576713.2 2/2
ACTTTAGAGTTCTTACAGGACAAGGGATAACAATAAGCCTCAAATGCAAGTTGAACAGCCAAGAACAGTCTCGACTTCTAGAATTTACATTTACGAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576713.3 3/2
GTACATGGGGTGGGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGC
+
FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFF-FFFF-F-FF--F-FFF
@SRR6576713.4 4/2
TCATTAAGGGGATGTCATATGATGTCTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTAAAATATTAATTTACAATTAATTTAAAAAGAAAATCAAATAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-F---F-----F-F-F----F-F--F-FF--FF---FFF-888-
@SRR6576713.5 5/2
GTATTTATACACATATTTTTTCAGTAAAGTCTATTTTTCAGTAGATGTCAGGTCTGTCTTCTCATGAGAGGACTAGTTTTCTTTTTTCAGTTTTTACTAT
+
FF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFF88FFFFFF

Starting FASTQC command


Processing SRR6576713_1.fastq

Printing command:
fastqc --outdir SRR6576713_1.fastq

Analysis complete for SRR6576713_1.fastq

Processing SRR6576713_2.fastq

Printing command:
fastqc --outdir SRR6576713_2.fastq

Analysis complete for SRR6576713_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 89M
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 C13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:41 SRR6576713_1.fastq
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:41 SRR6576713_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:47 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================