-----------------------
Start of variable list:
-----------------------
Sample_ID:
B7-MAA100039-3_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 19:42:19 EDT 2018
Running on node : scc-wl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790992
Current job name : Step_02_B7-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790992.1.w

Loading required modules...


List files in scratch directory:

total 109M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 36 root   root       12K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:42 SRR6576826_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:42 SRR6576826_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576826_1.fastq <==
@SRR6576826.1 1/1
GTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576826.2 2/1
CCTATCCCCTACGAGGCTACCCGGATCGATGACGCGAATTGGGGACATTCAAATGAGCATCCTAGTCACCGCGTTTAAAATGAACCTGCCGGCTGATCGT
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFF8FF8FFFFF8FFFFFFFFFFFFFF--F-FFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576826.3 3/1
TCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTACGTTATCGGAATTAACCAGACAAATCGCACCAC
+
-FFFFFFFFF-FFF8FFFFFFFFFFFFFFFF8FF8FFFFFFFFFFF-FFFFFFF-FFFFFFF-FF--FFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576826.4 4/1
GTGCAACTTCGGGGCACGAGGCTCAGAGCCCACATCCACCACGTAGATGCGGGAGGACATGAGACCAGGCAGTATCAGCTTGTTGCGTGACTTCGTGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576826.5 5/1
GTTCTATTCTGTTTGCTCTTGTGACCCCAGGAGAACTACAGAAGCAGTCGATGCTGCAGGAGATGCCGGAAAGGGACTCGCGGCGCAGGGACGAAGCAGT
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6576826_2.fastq <==
@SRR6576826.1 1/2
NATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576826.2 2/2
NCATATCATATCCAAGATAGTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCTG
+
#FFFFFFFFFFFFF8FFF-FFFFFF-FFFFF-FFFFF-FFFFF-FF-F--FFFFFFFFFFF-FF---FF-FFFF-FFF-FFFFF8FFF-FFFF-FFFFFF
@SRR6576826.3 3/2
GCTAGAGGACAAATTCATGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAAAATGTTTACATTAATCAAGGACGAAAGTCGGAGGTTCGAAG
+
-F-FFFF--8FFF8FFF-FFFFF8-FFFFF-FFFFFFFF-F-FFFFFFFFFFF-FF-F-FF-FFF--FF-FFFFFFF-F8F--FFFFFF-FFFF-FFFFF
@SRR6576826.4 4/2
TCTGGAGGCCATGAAAGGACCCCGAGAGGAGATTGTCTACTTGCCCTGCATTTACCGGAACACAGGCACCGAAGCCCCGGATTATTTGGCCACTGTGGAT
+
FFFFFFFFFFF-8FFF8FFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576826.5 5/2
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTAAATAATGAATTAACGACATTTATTATTTACGTTGGTACAACACATCCGACCCTGACA
+
F8FFFFFFFF8FF8FF8FFFFFFFFFFFFFFFFFFFFFFFF-F---FF----F-FF------FF-FFF-FF----F----FFF-F-F--F--F-8-8---

Starting FASTQC command


Processing SRR6576826_1.fastq

Printing command:
fastqc --outdir SRR6576826_1.fastq

Analysis complete for SRR6576826_1.fastq

Processing SRR6576826_2.fastq

Printing command:
fastqc --outdir SRR6576826_2.fastq

Analysis complete for SRR6576826_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 647M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 36 root   root       12K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 324M Oct 12 19:42 SRR6576826_1.fastq
-rw-r--r--   1 kkarri waxmanlab 324M Oct 12 19:42 SRR6576826_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:49 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================