-----------------------
Start of variable list:
-----------------------
Sample_ID:
N21-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 19:41:28 EDT 2018
Running on node : scc-yh3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790872
Current job name : Step_02_N21-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/8790872.1.y

Loading required modules...


List files in scratch directory:

total 48M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N21-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:41 SRR6576869_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:41 SRR6576869_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576869_1.fastq <==
@SRR6576869.1 1/1
CTGCTGGGAGGTGGTCCATCTCTGGAGCATCAAAGAAGTAAGCCAAGCAGCCCACAGAGAGCAGCACATGAAGCAACACGATTGTCACAATGGTGGCCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576869.2 2/1
ATGGGGAGCAGCGCCTTGGAGGTCCCGTGGATCTGTGTCTTGCTTCAACAGTGTTTGAACGGAACAGACCCGGGGATTCCCACTGTACTCGCTTCCAGCC
+
--FFFFFFFF-F8FFFFFFFF88FFFF8FFFFFFF8F8F88FFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576869.3 3/1
TGAGAAGGCCTACATCCCTGAGCTTCAGATCAGCTTTATGGAGCACATTGCCATGCCTATCTACAAGCTTTTACAAGACCTGTTCCCCAAGGCGGCAGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576869.4 4/1
CAGTCCAGCCAGCAGTTTGGGCACTTTACTCTGAAGCCCCTCTAGCTACTGAAGAATACCACCACCCCATGGCTGAAGACATGCTCCAGTTGTGACTGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576869.5 5/1
GTCTAATATCTAAATGTCATTCAAAGCATACTTGTAGGAAAAAAAAAAAGGTTTTTAACTTTTAAAAACATTTTGCATATCAGGGCACCTTCCCTGCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFF-FFFFFFFFFFFFFFFFFFF-FFFFF-FF-F-F--F-FFFF-FFF-F-FFF-

==> SRR6576869_2.fastq <==
@SRR6576869.1 1/2
ACTGTCATCTATGCCTATGCCTGGCTGGTCCCTCTGGCCCTCTGGGGCTTCCTCCTGTGGAGAAACAGCAAAGTGATGAGCATGGTTTCCTATTCCTTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576869.2 2/2
AGAGTGAGGCGCTCAAAGAGATACTCGCCCAGAGACCCCTGGGGCGCGCCAGTCTGCGCTGGTTGTGGCCCCGCCACCCTGCGGAGGTTGGTCAGATGGT
+
F-F-FFF8FFFFFFFFFFFFF8FFFFF8F8FFF8FFFFFF-FF-FF--FFFF-F-FF-FFFF--FF-FFFFF-FFFFFFF-FF--F-8FFFFFFFF-FF-
@SRR6576869.3 3/2
CCATACCACTGCCCCTGGTCACTACTGTGCTCTTGTGTACAAATGGCAAAGTCTGTGTGGGACTGGTAATCTTGCTTGCCTTCTGCAGATGAGAAAGATG
+
FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFF8FFFFFFFF-FFFFFF-FF8FF
@SRR6576869.4 4/2
CTATTACAGTCCTCTGGTCTAGAATGCAGGAATCTCCCATCAGCCCTAGTTGGCTGTTAGTGTTACAGCTCTCAGCATAGGTTTTCTGTGATCCTTGGTT
+
FFF-FFFFFFFFF8FFFF88FFFFFFFFFFF8F8FF--FFFF-FFFF-F-FFFFFFF-FFF--FFFFFFF-FFFFFF--FFFFFFFFFFFF-8-FFFFF-
@SRR6576869.5 5/2
AAACAGGACCTGTCCCAGAAGCTGTTAACTTCTGTAGTCCACACTTTCACCTGTGCAGACTAGTCATGGTGGAGTCCAGGAACCAAGATGTCTCCCGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFF-FF-FFFF-FFFFFFFFF-FFFF--FF-FFFFFFFFFFFFFFF-F88FFF8FFFFF-F

Starting FASTQC command


Processing SRR6576869_1.fastq

Printing command:
fastqc --outdir SRR6576869_1.fastq

Analysis complete for SRR6576869_1.fastq

Processing SRR6576869_2.fastq

Printing command:
fastqc --outdir SRR6576869_2.fastq

Analysis complete for SRR6576869_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 226M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N21-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 113M Oct 12 19:41 SRR6576869_1.fastq
-rw-r--r--   1 kkarri waxmanlab 113M Oct 12 19:41 SRR6576869_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:43 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================