-----------------------
Start of variable list:
-----------------------
Sample_ID:
E7-MAA100138-3_56_F-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 19:44:31 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791127
Current job name : Step_02_E7-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791127.1.linga

Loading required modules...


List files in scratch directory:

total 74M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 E7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  36M Oct 12 19:44 SRR6575842_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  38M Oct 12 19:44 SRR6575842_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575842_1.fastq <==
@SRR6575842.1 1/1
ACTTAAGACAGACTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGGAAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAAACAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575842.2 2/1
ATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATAGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTA
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFFFFF-FFFFF-F-FFFFFFFFFFFFFF
@SRR6575842.3 3/1
AGGTCTGCCCGAGGACCTCATCCAGAAAGGGAAGGACATCAAGGGGGTGTCAGAAATCGTGCATGAAGGGAAGAAAATCAAACTCACCATCACCTATGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575842.4 4/1
GTCCATCCCCCTCCATCAGACATGTCACAATAAACAGAGAATTCTGCCAGGCTCTGAAGAGGTTTGATTTTGTAAAATCCACTCTGCTTAAATCCGTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575842.5 5/1
GGCAGAACATGCGACCCTGGGCCTTCTGCTTACAGTGCCTATGAAACTACATACAGTATACATTAAAGCTCTTCAGAATAACGACATGAGGGGCCCTGTT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FF-

==> SRR6575842_2.fastq <==
@SRR6575842.1 1/2
NTCATTGTATATTGCCCACCTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTCGAGGCAGTGATTGACATTGGTTAGGTCAATGATATTTTCTCTAATG
+
#FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6575842.2 2/2
CCCAAAGACTTTGGTTTCCCGGAAGCAGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCAACGTTTATGGTCGGAACTACGACGGTAT
+
FFFFF--FFFFFFFFF8FFF8FFFFF-FF-FFF---FFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-F-FFF-8FFFF8FF-FFFFFFFFF88-
@SRR6575842.3 3/2
GTATTGGTGATTGTGTCTCCATTGAGTTCAGTCACGGACTTTATGCCTTTGAAAGTTGTCACCATTTTATTGTCACCTTCCAGCTTGACGACTGCCTTGA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFF8
@SRR6575842.4 4/2
GCTCTTGCATGAGAAGGAAGTCCAGTTTCTGGATAAAGGATCGGAGAACAGTTTCATTGACCTTGGAGGCAAGAAGCAGTATGCAGATTGTTCAGAGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8FF
@SRR6575842.5 5/2
GAGATAATCCGAGACTGGTTGGATTGGACCTATTCCGCAGCGACGTTTTCTGTTTTCCTCAGCATCCTTTACTACTACTCCTCGCTGAGCAGATTTCTCA
+
-FFFFFF-F8FFFFF-8F-FF8FF---FFF-F-FFFFFFFF-FF-FFFFF-F-FF-F-FFFFFFF-FF-FF-FFFFFFFFFFF-F-FF-FFFFF--FFFF

Starting FASTQC command


Processing SRR6575842_1.fastq

Printing command:
fastqc --outdir SRR6575842_1.fastq

Analysis complete for SRR6575842_1.fastq

Processing SRR6575842_2.fastq

Printing command:
fastqc --outdir SRR6575842_2.fastq

Analysis complete for SRR6575842_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 437M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 E7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 219M Oct 12 19:44 SRR6575842_1.fastq
-rw-r--r--    1 kkarri waxmanlab 219M Oct 12 19:44 SRR6575842_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:15 EDT 2018
0 hours, 0 minutes and 44 seconds elapsed.
==========================================================