-----------------------
Start of variable list:
-----------------------
Sample_ID:
G5-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 19:41:28 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790790
Current job name : Step_02_G5-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/8790790.1.linga

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576361_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576361_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576361_1.fastq <==
@SRR6576361.1 1/1
GGTGTGGGTGTGTGTGTGTGTGTGTGTCAGCAGGGGTGGAGCAGAAGGAGTTGAATTCAGGGTATATATATATATATATTCCCTGAACATGGCTTCTGGG
+
FF-F-F-FFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFFFF8FFFFFFFFF-FFFFFF--FFFFFFFFFFFFFF-FFFFFFFF-FFFFFF--FFF-FFF
@SRR6576361.2 2/1
ATGGTAATGTGGGGAGAGGGAAATCATGATTTCTTAGGCTAGATCTATCCTGTTAGTCTAGCTTATGATTAAAATAGGAAGCTAAAACATACTGATTAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576361.3 3/1
GTAATAAGTTATTCTTGCTTTGCTATTTGTATGTCAGCACATTATTGTCACTGCTGCACTATTAATAAGACAATTAGTTGTGAATGTGTTAACTCAAAGG
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-
@SRR6576361.4 4/1
GCTTGCGTCCATAGCAACAGAAATAGGCCCCACAGTCGCCACAGCCTTCATGAGGGCTTTCTCTTGCTGAGGGATATCCACGAACCCTGTGTCATTAGCC
+
FFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFF
@SRR6576361.5 5/1
GCTTGCGTCCATAGCAACAGAAATAGGCCCCACAGTCGCCACAGCCTTCATGAGGGCTTTCTCTTGCTGAGGGATATCCACGAACCCTGTGTCATTAGCC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF

==> SRR6576361_2.fastq <==
@SRR6576361.1 1/2
NCTTCAGAGGACCTGAGAGGAGAGAAACGCAGGGCCCTGCTTCAGATCCCACCTCCTCTGCAAAGGAACAAACGAGACCAGGAAAGGGGAGACACAGGGA
+
#FF-FFFFFFFFF8F-F-FF8FFF-FFFFFFFFFFF--FF-FFFFFFFFFFFFFFFFFFFFFFFF-F--FF--FFFF-F-FF-FFFFFFFFFF-F--FFF
@SRR6576361.2 2/2
NATTATAACTGTGTGCTGAGGAAGGAGCTCAGAGATTTAGGCTTGTGGTACAAGCACTGTATCAAGTGAGCTTCCACTGCAGGTTTGTTAGTATAGTCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6576361.3 3/2
CAGTGTTATCAACAGCCGTGTGTCTGATGGGGCAGCTCCTGCCACTGTCCACCACTCACCTCAGGGGTCACTAATTTTAGTGATCCCTGGGCACCTCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576361.4 4/2
TAGCTACTCCAAAATTTGATCAAACCTTTAGTGCAGAGTGGCACCAGTGGAAGTCCACACACAGAAGACTGTATGGCACGAATGAGGAAGAGTGGAGGAG
+
FFFFFFFFFFFFFFF-FFFF8FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFF-FFFFFFF-F8FFFFFFFFF-F-FF8FF8FF
@SRR6576361.5 5/2
TAGCTCCTCCAAAATTTGATCAAACCTTTAGTGCAGAGAGGCACCAGTGGAAGTCCACACACAGAAGACTGTATGGCACGAATGAGGAAGAGTGGAGGAG
+
-FFFF-F-FFFFFFF-FFF8FF-FFFFFFFF-F-F-FF----FFFFF-FF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F--FFF-8---

Starting FASTQC command


Processing SRR6576361_1.fastq

Printing command:
fastqc --outdir SRR6576361_1.fastq

Analysis complete for SRR6576361_1.fastq

Processing SRR6576361_2.fastq

Printing command:
fastqc --outdir SRR6576361_2.fastq

Analysis complete for SRR6576361_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 131M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  66M Oct 12 19:41 SRR6576361_1.fastq
-rw-r--r--   1 kkarri waxmanlab  66M Oct 12 19:41 SRR6576361_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:49 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================