-----------------------
Start of variable list:
-----------------------
Sample_ID:
B7-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 19:42:19 EDT 2018
Running on node : scc-wg2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790990
Current job name : Step_02_B7-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/8790990.1.w

Loading required modules...


List files in scratch directory:

total 40M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 25 root   root       80K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:42 SRR6576158_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:42 SRR6576158_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576158_1.fastq <==
@SRR6576158.1 1/1
GTCAGAGAGGAACCCTTCTCTGAGGATGGACAGTACTCACGCTACAAAGTCCTGTTTGCTGATTCTTCTTGTGGCCCTACTGTGTGCAGGAAGAGCTCAG
+
FFFFFFFFFFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576158.2 2/1
CTTAGAGGGACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGACTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576158.3 3/1
TCTATACTCTATGGCTCATTAGGATCTATTGTGACTGGACTTGGACATTTCTTGGTGACCAGTGAGTATTTTCCTTAAATTAAAACAGCTCTATTATAAT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576158.4 4/1
TCTTCATCCAGGGTACTTGGAGGATACCCATTTCGCAGGTTCCTTTCTCTGTGTGACACTGAAACCCTGCCGGGCAGCAATGAATGTGATCCTCACAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576158.5 5/1
GGAATAAGATCCTCAGTATACAAGCTTATTGTAAGGCTGAGTTAAGTTTTATTTATTTGCAGTGGGACGTGATCTGGTTTTCTTTTTGAAACAAAATGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576158_2.fastq <==
@SRR6576158.1 1/2
AGATACTTATGTGTGGATGGTGATAGTATAATACCTTGGAATACTGCCTGTTGCATGTGCTGGGCACATGCCTCCAGGGCCAAGAATAGAGATCCACAAC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFF-FFFFF-FFFFFFFFFFFFFFFF-FFFFFFF8FF
@SRR6576158.2 2/2
GGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576158.3 3/2
CCTTGTAAGAATGAAAAAGAAAGTAAGCTACTAGTTCCTATATATGAGCAACCTAAGGAATTTTAATTCACAGATTTCCAAAATGCTTATAAAGGACTAT
+
8FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFF8FF
@SRR6576158.4 4/2
TCCCTGCACAAAAGACCAACAGGGCAGTGTCTTTGCCTTTTTCTGTCGTGTGCCCTGATGCTAAGACCCAGTGTCCCGATGATTCTACCTGCTGTGAGCT
+
FFFFFFFFFFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8FFF
@SRR6576158.5 5/2
TATCTCAACAGTATAGTTATTGGTTTTCTCACCTCTAAAGTGCCTTTGCCTCATCCATCTTTTAAAAAACATTTTGTTTCAAAAAGAAAACCAGATCACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-

Starting FASTQC command


Processing SRR6576158_1.fastq

Printing command:
fastqc --outdir SRR6576158_1.fastq

Analysis complete for SRR6576158_1.fastq

Processing SRR6576158_2.fastq

Printing command:
fastqc --outdir SRR6576158_2.fastq

Analysis complete for SRR6576158_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 208M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 25 root   root       80K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B7-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:42 SRR6576158_1.fastq
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:42 SRR6576158_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:33 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================