-----------------------
Start of variable list:
-----------------------
Sample_ID:
P2-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 19:42:18 EDT 2018
Running on node : scc-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790903
Current job name : Step_02_P2-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/8790903.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 48 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.7M Oct 12 19:42 SRR6576739_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:42 SRR6576739_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576739_1.fastq <==
@SRR6576739.1 1/1
CTACTGGGGATCAAACTTAAGCAGATAGGGTTGTCAGCAAGCACCTTAACTCTGAGCCATCATTTGGGCTCAGAAGTAACTTTAAAGAGACTGAATTCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576739.2 2/1
GTACATGGGACTCAGTCACAAGTCACTCAGTTGCAAGCATCTCATCCTTGTATGGCAGCAGCTAAAGGCCTTAAGTCTCATGGGCTCAGACATTGCAAAT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576739.3 3/1
GAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTCGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFF
@SRR6576739.4 4/1
AGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576739.5 5/1
AAATGCAGCTGTTCTCAAAGGCAAAAGTCAGAAATACAGATTCCTCTAGAGCCAGAGTTACAGATGGTCATGCATTACCCAAGAGGGTGCTGAGAACTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576739_2.fastq <==
@SRR6576739.1 1/2
NAGCACACCTGAGACCTAGCTACAGAACAACAGCAGAGTGTGACACCCTGAAAACATTTCCCTAGCACTCCTCTGAGTACATTAATAAAGTCCTTGACAT
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFF--FFFFFFFFF-FFFFFFF8FFFF-FF-FF-F-FF
@SRR6576739.2 2/2
CATGTGCACTTGAGTACAAGAGCTCTTGGAAGCCAAAGGTATTGGATTCCCCTGGAAGTAAGAGGGACTGTGAGTAGTCTGACATGGGTACTGGGAACTG
+
FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576739.3 3/2
TTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAG
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576739.4 4/2
GGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576739.5 5/2
GAGTATGGTACCCTTGAGTATAGTACCCTTGAGTGTGGTACCCTTGAGTGTGGTGCCCTTGAGTGTGGTGCCCTTGAGTGTGGTGCCCTGAGTATAGTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFF-FFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576739_1.fastq

Printing command:
fastqc --outdir SRR6576739_1.fastq

Analysis complete for SRR6576739_1.fastq

Processing SRR6576739_2.fastq

Printing command:
fastqc --outdir SRR6576739_2.fastq

Analysis complete for SRR6576739_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 109M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 48 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:42 SRR6576739_1.fastq
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:42 SRR6576739_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:31 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================