-----------------------
Start of variable list:
-----------------------
Sample_ID:
B12-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 19:42:20 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790960
Current job name : Step_02_B12-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/8790960.1.linga

Loading required modules...


List files in scratch directory:

total 42M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B12-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:42 SRR6575355_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:42 SRR6575355_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575355_1.fastq <==
@SRR6575355.1 1/1
GCTAACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAACTTCTTAGAGGGACAAGTGGCGTTCAGCCACCCGAGATGGAGCAATAACAGGTCTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFF--FFFFF-FFFFFF
@SRR6575355.2 2/1
GGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAG
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575355.3 3/1
GTATAATGGTAATTAGTAGGGCTTGATTTATGTGGTTTCGTTTACCAACTATAAGGCTATGAAGAGCTCATGTAATTGAAACACCAGATGCACTGTCTCT
+
FFF-FFFFF-FF-FF-FF8FFFFFFFFFFFFF8FFF8FFFFF8FFF--FFFFFFFFFFF--F-FFFFFFFFFF-F--FFFFFFFF-FF-FF-F-F-FFF-
@SRR6575355.4 4/1
GAGTACATGGGACATCCTGTCATTCAAGCTCTGATTGGCTGTTCCAAAGTTGGCTTAGACAGCTACATTGACTATCTCTGTGATCCCACATGCACATAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575355.5 5/1
GTGTTGGAAAGAATGGAGACGGTTGTTGATTAGGCGTTTTGAGGATGGGAATAGGATTGAAGGAAATATAATGATGGCTACAACGATTGGGAATCCTATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF

==> SRR6575355_2.fastq <==
@SRR6575355.1 1/2
CCCAAGATCCAACTACGAGCTTTTTAACTGCAGCAACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCAACAGACTTGCCCTCCAAAG
+
FFFFFFFFFFFFFFFFFFF88FFFFFFFFFFF-FFFFFFFFF-FFFFFFFFF-FFFFFFF-FF-FFFFF-FFF-FFFFFFF-FFFFFFFFFFFFF-FF-F
@SRR6575355.2 2/2
ACCTAAGACAGACTATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTG
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575355.3 3/2
AGCATCAGGTGTTTCAATTACATGAGCTCATCATAGCCTTATAGAAGGTAAACGAAACCACATAAATCAAGCCCTACTAATTACCATTATACCTGTCTCT
+
FFFFFFFFFFF-FFFFFF-FF8F8FFFFFFFFFFFFFF-FFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FF
@SRR6575355.4 4/2
GTATTTGCCAATGCCTAGGTTTGGGGTACAGACACATAAAGAGGAGTCACCAGGGAAGAAGAATAAAGGCAGATTCCAGGTTCAGAAATATGCACAGATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575355.5 5/2
GAGTACATGGGATGCCACAACTAGATACATCAACATGATTTATCACAATTATCTCATCAATAATTACCCTATTTATCTTATTTCAACTAAAAGTCTCATC
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575355_1.fastq

Printing command:
fastqc --outdir SRR6575355_1.fastq

Analysis complete for SRR6575355_1.fastq

Processing SRR6575355_2.fastq

Printing command:
fastqc --outdir SRR6575355_2.fastq

Analysis complete for SRR6575355_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 271M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B12-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 136M Oct 12 19:42 SRR6575355_1.fastq
-rw-r--r--   1 kkarri waxmanlab 136M Oct 12 19:42 SRR6575355_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:40 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================