-----------------------
Start of variable list:
-----------------------
Sample_ID:
N15-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 19:41:26 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790708
Current job name : Step_02_N15-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/8790708.1.linga

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576802_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576802_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576802_1.fastq <==
@SRR6576802.1 1/1
GTCTGGTCTCAAACCTGGCAACCTATGAAACCCTGAATATCTCCTGGGCTTCTCAAAGTGGTGAACCACTGGAAACCAAAATTAAAATCATGGAAAGCCA
+
FFFFFF-FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576802.2 2/1
CTCCCGGCTCGGGAGTCGCATCCTCAGGAGTGGTGTAGCGAGCGAACTCTGGAAAGTAGTCCTCAATCTTCGATTTGCCAGCGAGGACTTTCTCAGCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576802.3 3/1
GCTCAGGACCACTCAGTGGTGGCTCCAACCCACTCAGTGGCCTGCGCTGTGGGAGCTGCTGACCAATCCTCAGTGGCTGGCTGTGCACTCCAGTCTTCCG
+
FFFFFFFF-FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576802.4 4/1
GCGTAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTGAGTGTGTGTGTGT
+
8-F---F-FFFFF8F8FFFFF8FFFFFFFFFFF8FFFFF8F8F-FFF--FFFF-FF-----FFF-F-FFFF-F--FFFFFF---F---FFFFFFFFFFF-
@SRR6576802.5 5/1
GTCATAGGACCTCAAAGAGCCAGACATATCCAGGTGGTCACTGGGGTGACTGAGAGACAGTAGTAGGGGGTGATGTTAGTCAAGAGCCTCGCTATACAGG
+
FFFFFFFFFFFFFFFFF8FFFFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF

==> SRR6576802_2.fastq <==
@SRR6576802.1 1/2
CATACTTCTCTTGGGGCAAGAGTTGCCCTCTCTGAAGCCACTGCACACTGATGTCTGCAGGAGAGAAGCCCTTCACCAGGCAGGTGACTGTGGCTGACTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576802.2 2/2
GCCGTGTCCTGACCTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCACATGTTCGATGTGGGCGGCCAGTGCGATGAGCGCCGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576802.3 3/2
ACCGATCCCAGGGCTGACCATCAGCCACTCACAGAGGCCTCTTATGTCAACCTGCCCACCATTGCTCTGTGTAACACAGATTCTCCCCTGCGCTATGTGG
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FF88F
@SRR6576802.4 4/2
TACCTGCAGCAAGCTGCACTTCATTTCTTGGCCTCATGCTGGGACTCTCTCCTCTTACAAAACTTTATTTCTTCGTGCATTGGTAGAACAAGCTGTCTGG
+
FFFFF8FFFFFFFFFFF8FFFFFFFFFFFFFF-FF-FFFFF-F-F--FF--F-FFFF-FFFFFFFFFF--FFFF-F-FFF-F-FFFFFF-F-F--FFF8F
@SRR6576802.5 5/2
ATCTTAGCTGCACAGAGAAGAACATGCTGATGTTCAACTGGGTTGGGAAAGGACTTTGAAAACTAAGGAAGCTGTATGCAAGCAAGCACTACAAACACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFF-FFFFFFFFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6576802_1.fastq

Printing command:
fastqc --outdir SRR6576802_1.fastq

Analysis complete for SRR6576802_1.fastq

Processing SRR6576802_2.fastq

Printing command:
fastqc --outdir SRR6576802_2.fastq

Analysis complete for SRR6576802_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 138M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 N15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  69M Oct 12 19:41 SRR6576802_1.fastq
-rw-r--r--   1 kkarri waxmanlab  69M Oct 12 19:41 SRR6576802_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:50 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================