-----------------------
Start of variable list:
-----------------------
Sample_ID:
O4-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 19:49:50 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791356
Current job name : Step_02_O4-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/8791356.1.linga

Loading required modules...


List files in scratch directory:

total 38M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 102 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 O4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  19M Oct 12 19:49 SRR6576694_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  20M Oct 12 19:49 SRR6576694_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576694_1.fastq <==
@SRR6576694.1 1/1
TGAGAGCTAAGCTGACTTCCCCAAAGCCACGTGACTTTACTGGTCACTGAGGCAGTGCATGCATGTCAGGCTGCCTTCATCTTTTCTATAAGTTGCACCA
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576694.2 2/1
CTTCAGTGGCTCTCTGGATTTCTTCAGCGATGCCTTCTTCAACTCGGCAGTGCAGAAGGCCACACCCGGTGCGCAGAGGTATTCTCAGACAGGCAACTAT
+
-F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576694.3 3/1
GTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAATTATTAGGGTTCATGTTCGTCCTTTTGGTGTGTG
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576694.4 4/1
GTCCTGCAGCGGAACAAGATATAAGGTATGGTGACAGCTACTATGCAGCAAAGGGAGATGATGAAGATTATGGCAAAGATTGGCAGGTTCCTCCCTGAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576694.5 5/1
GTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAATTATTAGGGTTCATGTTCGTCCTTTTGGTGTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF

==> SRR6576694_2.fastq <==
@SRR6576694.1 1/2
NGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAACAAAAAAAATTATTTTAATAATAGGTAAAAATAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---F----FFFF-F----F-FF----F----8FFFF----FF--FF--8F-F
@SRR6576694.2 2/2
CTTCAGGAAGGTCCTCACGAAGGGGTCGATGCGCACGAACTCCAGCTGAATGTCATCACCATCAAAGGGGACCCACTTGCCATTGGAGAGCTGTTCTATG
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-8FFFFF
@SRR6576694.3 3/2
ATCTTATTTCAACTAAAAGTCTCATCACAAACATTCCCACTGGCACCTTCACCAAAATCACTAACAACCATAAAAGTAAAAACCCCTTGAGAATTAAAAT
+
FFFFFFFFFFFFFFFF8F-FFFFFFFFFFF--FFF-FFFFFFF-FFFFFFFFFFFFFFFFF-F-FFFFFFFFF-F-FFF8F---8FFF-FFFF-FFFFFF
@SRR6576694.4 4/2
ACCTAATAGTGCTCACCTATGGCCACCCCACCCTAAAAACACCTGAGAGTGTGACAGGGACCTGGAAAGGAGATGTGAAGATTCAGTGCATCTATGATCC
+
FFFFFFFFF8FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576694.5 5/2
ATCTTATTTCAACTAAAAGTCTCATCACAAACATTCCCACTGGCACCTTCACCAAAATCACTAACAACCATAAAAGTAAAAACCCCTTGAGAATTAAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6576694_1.fastq

Printing command:
fastqc --outdir SRR6576694_1.fastq

Analysis complete for SRR6576694_1.fastq

Processing SRR6576694_2.fastq

Printing command:
fastqc --outdir SRR6576694_2.fastq

Analysis complete for SRR6576694_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 202M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 O4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 101M Oct 12 19:49 SRR6576694_1.fastq
-rw-r--r--    1 kkarri waxmanlab 101M Oct 12 19:49 SRR6576694_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:15 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================