-----------------------
Start of variable list:
-----------------------
Sample_ID:
K9-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 19:46:11 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791274
Current job name : Step_02_K9-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/8791274.1.linga

Loading required modules...


List files in scratch directory:

total 34M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 101 root   root      180K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 K9-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  17M Oct 12 19:46 SRR6576458_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  18M Oct 12 19:46 SRR6576458_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576458_1.fastq <==
@SRR6576458.1 1/1
GAGTACATGGGGGGAGTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGC
+
FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576458.2 2/1
CCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAAGTTTGCACAACTAAGCGAGGAGCATGGAATCGTTAGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576458.3 3/1
CCCTGGAAGAGATTCAGAAGCACAAAGACAGCAAGAGCACCTGGGTGATCCTGCATCATAAGGTGTACGATCTGACCAAGTTTCTCGAAGAGCATCCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576458.4 4/1
CAAAGAGGGGGCTCTGAGTGTGTTCTTCAAATATTATGAAAAGGAAAGGGTGATCGAAGCGCACGATAGGGGGCATAGAATAAGGAACGGCTAGTAAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF8FFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576458.5 5/1
ACCCTAGTGTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTG
+
FF-FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFF

==> SRR6576458_2.fastq <==
@SRR6576458.1 1/2
GAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTC
+
FFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FF-FFFFFF
@SRR6576458.2 2/2
ATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAGACACGATGGAAAGCAGATCACAGAACTTCTTACTGGATGCTGTATGGATAGGAAGGACTGATCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576458.3 3/2
GACAAGTCAATCTTCTGCCATGTAGAGGCGATACATCAGAGCTACAGCCAGGGCTGAGATGGCTGGGATCACCCAGTTGGTCCACCAACTGGAATTAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576458.4 4/2
TTCTGGAAGAGGCCAAGAACCATTATCAGGCAGAAGTCTTCTCTGTCAAATTTGCTGAGTCAGTGGAGGCCAAGAAAGTGATTAATGATTTTGTGGAGAA
+
F-FFFFF8FFFFFFFFF8FFFFFFFFFFF8FFFFFFFFFF----FFFFF-F-FF--FFFFFFF-F--FF-FF-FF-F-FF-FFFFFFF-FFFFFF8F8F-
@SRR6576458.5 5/2
CTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGG
+
FFFFFF8FFFFFFFFFFFFFFF8FF88FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF8FFFF-FFFFFFF8

Starting FASTQC command


Processing SRR6576458_1.fastq

Printing command:
fastqc --outdir SRR6576458_1.fastq

Analysis complete for SRR6576458_1.fastq

Processing SRR6576458_2.fastq

Printing command:
fastqc --outdir SRR6576458_2.fastq

Analysis complete for SRR6576458_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 184M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 90 root   root      180K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 K9-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  92M Oct 12 19:46 SRR6576458_1.fastq
-rw-r--r--   1 kkarri waxmanlab  92M Oct 12 19:46 SRR6576458_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:37 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================