-----------------------
Start of variable list:
-----------------------
Sample_ID:
H12-MAA100041-3_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 19:46:08 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791223
Current job name : Step_02_H12-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791223.1.linga

Loading required modules...


List files in scratch directory:

total 71M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 92 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H12-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:46 SRR6575516_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:46 SRR6575516_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575516_1.fastq <==
@SRR6575516.1 1/1
GNGCGGGGCCCACTACTGTGGGCTGCAGCCAGGGGTCCCTCCAGCCGGAAGCCATCAGGATGTGTGGCCATGGTGACTCGANGGCTCTGTGGTCTGGTCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575516.2 2/1
ATCCTCTTCTGCAATACGGTCCAACCATTTCCAGATCCGTCGATTTCACAGTACACTAAGAACTGCTGCTTAGCTTTCAAAGGTCGAATGAAGTAAAGTC
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFF-FFFFFFF
@SRR6575516.3 3/1
CAGTCATTCTTTCTCCAGTGGGATCAAGTGCTCTGGGATGTCTACCTGGAATATATCCTTTCCCCCTTTCCTAGGTATGGGCTCCAGTAACCACCTGGGG
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFF
@SRR6575516.4 4/1
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAATAACACGTGTTTTTAAAAACCAAATGAATGTTACAGGGTAAAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-------FF---F-F-FFF---FF-FFFF--FF--------F-FFFF---
@SRR6575516.5 5/1
CGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGATCAATCTCGGGTGGCTGAACGCCACTTGTCCC
+
F8-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF--FFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFFF-FFFFF-FFFFFFFFFFFFFF

==> SRR6575516_2.fastq <==
@SRR6575516.1 1/2
NGGTGNGGGTGGTGGGCTATGGCCGCCTGGGACAGTCCCTTGTGTCCCGCCTTCTGGCTCAGGGATCAGAACTGGGCCTAGAACTTGTTTTTGTGTGGAA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575516.2 2/2
NAGATTGTCAGGAAATTGCCAACAAGGGCGCCAAAGAAAGTGGACTTTACTTCATTCGACCTTTGAAAGCTAAGCAGCAGTTCTTAGTGTACTGTGAAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6575516.3 3/2
GAAATACACCATTGCCATCCACATTGCTCACAAGGACTGGGAAGATGATGAATGGCAGGAAGTGCTCATGGAGAGGTTGGGGATGACCTGGACACAGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575516.4 4/2
NTCCAAGACGGTGCCCTGGTCCAGCACCAGCAATGGGACGGGAAGGAGAGCACGATAACAAGAAAACTGAAGGATGGGAAGATGATCGTGGAGTGTGTCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8FFFFFFFFFFFFFFF-FFFF
@SRR6575516.5 5/2
GCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAATACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGAAGCG
+
F8FFF-FFFFF-FF8F8FFFFFFFFFFFFFFF--F-FF--FFFFFF-F-FFFFFFFFF-F-FFF-FF-FFFFFFFF-FFFFFF-8FFFFFF8FFFF-F8F

Starting FASTQC command


Processing SRR6575516_1.fastq

Printing command:
fastqc --outdir SRR6575516_1.fastq

Analysis complete for SRR6575516_1.fastq

Processing SRR6575516_2.fastq

Printing command:
fastqc --outdir SRR6575516_2.fastq

Analysis complete for SRR6575516_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 376M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 78 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H12-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 188M Oct 12 19:46 SRR6575516_1.fastq
-rw-r--r--   1 kkarri waxmanlab 188M Oct 12 19:46 SRR6575516_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:47 EDT 2018
0 hours, 0 minutes and 39 seconds elapsed.
==========================================================