-----------------------
Start of variable list:
-----------------------
Sample_ID:
H11-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 19:46:08 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791219
Current job name : Step_02_H11-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/8791219.1.linga

Loading required modules...


List files in scratch directory:

total 70M
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 H11-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  34M Oct 12 19:46 SRR6575513_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  37M Oct 12 19:46 SRR6575513_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575513_1.fastq <==
@SRR6575513.1 1/1
AACTTGTACAGACACTGAGAAAGTTCAGTGGATGTACTGAATCTTTAACCAGGCATCAAAACCAATCTATTAAGCCCCTGTTTCATCTCAATTTTACTCA
+
8F-FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF--F-FFF--FF-FF--FFFFFF
@SRR6575513.2 2/1
TCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575513.3 3/1
GTCCACTGGGCATCACCCGGATCTTCAACAGTGGGGCTGACCTCTCCGGAATCACAGAGGAGAATGCTCCCCTGAAGCTCAGCCAGGCTGTGCATAAGGC
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575513.4 4/1
ACTTTATTTGGGGGAAGTGACTGCACCGGCAATTTCTGTTTGTTCAAGTCCACCACCAAGGACCTTCTGTTCAGGGATGACACCAAATGTTTCGTTAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575513.5 5/1
CTCTTCTATCATGGTCAAGTTCTGGGTCACGGTCAGGGGCAGGAAGAAGATGATGCTCATACTTCCTGTCAAGGGCAGCTGGGCAATCTTGCAGTTGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575513_2.fastq <==
@SRR6575513.1 1/2
NATAATAATTCCAAAGACAAAGTCTCTCATAAAGCCCTTTCTGCCATGGAGATCACAGCCCAGTCAATTATCTATAGTTTTGCTGGGTCTGAAACCACCC
+
#FFF--FFFFFF8F8-FFFFF8FF-F-FFFFFFFFFF-FFFF-FF--FFFFFF-FFFFFFFF-FFF-FFFFF--FF-F--F-F--FF--FF-FF88-F-F
@SRR6575513.2 2/2
NCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATA
+
#FFFFFFFFFFFFFF-FFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFF-FFF-FF-F8-
@SRR6575513.3 3/2
NATTTATGTGTGGGATCTACCACTTTTCCCACAAAGAGGGGGCTCTGAGAGTGTTCTTCAAATATTATGAAAAGGAAAGGGCGGTTGAAGTGCAAGATAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6575513.4 4/2
GCAGCGAAGACTACACCAGTTAGCCCCAACCCCTCAGGGCATGAAGACCAAGAGAAGCCCATGGGCCACGGGAGGGAGCATCTGTCTCCACCACAGTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575513.5 5/2
GCCCTCAGCATCCTTCTCCTTGGCGTGGCTTACTTCAAGGGGCAGTGGGTAACCAAGTTTGACTCGAGAAAGACGACCCTCCAGGATTTTCATTTGGACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575513_1.fastq

Printing command:
fastqc --outdir SRR6575513_1.fastq

Analysis complete for SRR6575513_1.fastq

Processing SRR6575513_2.fastq

Printing command:
fastqc --outdir SRR6575513_2.fastq

Analysis complete for SRR6575513_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 404M
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 H11-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 202M Oct 12 19:46 SRR6575513_1.fastq
-rw-r--r--   1 kkarri waxmanlab 202M Oct 12 19:46 SRR6575513_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:50 EDT 2018
0 hours, 0 minutes and 42 seconds elapsed.
==========================================================