-----------------------
Start of variable list:
-----------------------
Sample_ID:
J4-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 19:46:10 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791266
Current job name : Step_02_J4-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/8791266.1.linga

Loading required modules...


List files in scratch directory:

total 16M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 113 root   root      164K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 J4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 7.2M Oct 12 19:46 SRR6576467_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab 7.9M Oct 12 19:46 SRR6576467_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576467_1.fastq <==
@SRR6576467.1 1/1
GGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576467.2 2/1
CAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCG
+
FFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576467.3 3/1
CATGGGATGCCACAACTAGATACATCAACATGATTTATCACAATTATCTCATCAATAATTACCCTATTTATCTTATTTCAACTAAAAGTCTCATCACAAA
+
FFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576467.4 4/1
ACTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFF
@SRR6576467.5 5/1
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTCCGAAAAAATAAATGGAGAAGTATTGGAAAAGTAAGAATACGTAAACAAAATTTCATTATCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-8888--8-FF-F--F-F------------FFF-F-F-F--------FFFF----FF--------

==> SRR6576467_2.fastq <==
@SRR6576467.1 1/2
GGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGTAAGAGTCCTGGATTGTTATTTTTCGT
+
FFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFF---FFFFFFFFFFF-FF-FFFFFFF-FFFF--FFFFFFFF-F-FFFFFF-F---FFF--F----FF-
@SRR6576467.2 2/2
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCCCGGCCGGTACAGTGAAACTGCGA
+
FFFFFFF-FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFF-FFFFFFFFFF-FF-FFFF-FFFFFFFF-8FFFFF
@SRR6576467.3 3/2
GTAAAATAATAAATCTAATGGTAGCTATTGGTGGGCTAATAATTATTAATACTAGAGTATCACCTCCGATTAGGTTTAATAATAAGTGTACTGCAGTTAT
+
F-FFFFFFFFF-F88FFFF8FFFFFF--FFFF----FFF-F-FFFF-FFFFFFF-FF-F-F-FFF-F-F--F-FF-FF-FFFFFF-FFF---FFFFF-F-
@SRR6576467.4 4/2
CCTTCCCGGGGGGGGATGCGTGCATTTATCAGAACAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTAGGTGCC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF--FFFFFFF-FF-F--
@SRR6576467.5 5/2
ATCTATGGTTCTACATTCTTCATGGCTACTGGATTCCATGGACTCCATGTAATTATTGGATCAACATTCCTTATTGTTTGCCTACTACGACAACTAAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFF-FFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576467_1.fastq

Printing command:
fastqc --outdir SRR6576467_1.fastq

Analysis complete for SRR6576467_1.fastq

Processing SRR6576467_2.fastq

Printing command:
fastqc --outdir SRR6576467_2.fastq

Analysis complete for SRR6576467_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 93M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 J4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  47M Oct 12 19:46 SRR6576467_1.fastq
-rw-r--r--    1 kkarri waxmanlab  47M Oct 12 19:46 SRR6576467_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:29 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================