-----------------------
Start of variable list:
-----------------------
Sample_ID:
K9-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 19:41:27 EDT 2018
Running on node : scc-wb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790841
Current job name : Step_02_K9-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/8790841.1.w-long

Loading required modules...


List files in scratch directory:

total 99M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:41 SRR6576521_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:41 SRR6576521_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576521_1.fastq <==
@SRR6576521.1 1/1
GTCTTAGTTCAAGAAGTCTAAATGTGAATAATTTCCTTGTTACTCTGCCCATTAAAATGACACAGGCCAGTTTTTTTTAATAGCCAATTAATCGGTGCAC
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFF-
@SRR6576521.2 2/1
GAAGTTTGTCATGCAGGAGGAGTTCTCGCGAGATGGCAAGGCTCTTGAACAGTTCCTGCAAGAATACTTTGATGGCAACTTGAAGAGATACCTGAAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576521.3 3/1
GTAGTAGGTTGAGATTTTGGACGTAATCTGTTCCGTACGTGTTTGAAACTTTTACTAGTAGGGCTAGTCCTACAGCTGCTTCGCAGGCTGCGAAAACTAA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576521.4 4/1
GCCCAGGCCCTGCCTCCTGCTGGGGCCGAAAATAGCAACTCTGACCCGAGGGTTCCGATCTATGACCAGGGTGGTCCTGTGGAAATCTTGCCCTACCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576521.5 5/1
GCACCCAGACGGCTGGCTTCTCAGGCTGGAGTGATGGCGTAGGTAGGTGTGCTGAGCTCAGCCGTCTGCCCTTGAATCGATGCCCTTTGATGTGTGCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576521_2.fastq <==
@SRR6576521.1 1/2
NTGTAGATGTAGATTGTTTAATCTACAGCAAAAATGTACTAGATTTCGTCTGTCATTAACACTGCTAAGCTATTTAAAAACACGGGAAGATAGGTACCTG
+
#---F--FF8FF8FF-FFFF88FFFFFFFFFFFF-FFF-FF-FF-FF-F---FF-FF-FFFFFFF-FFFFF-F-FFFFFF--F---FF--FFF-FFF8F-
@SRR6576521.2 2/2
ATTTGGATCTTTGCTGAGTTTTTCTCCCAGCTCTTTATACTTGGGTTCCAGATTCTTACAGTGGCCACACCAAGGGGCGTAAAATTCAATCAGCACGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576521.3 3/2
CCTTCTCACTATCACTTCTAGGGACACTTATATTTCGCTCTCACCTAATATCCACATTACTATGCCTGGAAGGCATAGTATTATCCTTATTTATTATAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576521.4 4/2
CAGCTGCCCCATGAAACTGAAGTTGGGGGAGATGACTCCCCGACGTTGCTTAACAAAGTCAAAGGCCTCGTCCAGCCGTACCCGGTGGCTCTGAATCAGG
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576521.5 5/2
AAACAGGGGTCACTATACTTTGCAAGACGGGGAAAAATAAAATTAAAAAAAATCTTTCCTTTTAATATAAAACAATATAATCACAATACCAGAATGTGGA
+
8FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF

Starting FASTQC command


Processing SRR6576521_1.fastq

Printing command:
fastqc --outdir SRR6576521_1.fastq

Analysis complete for SRR6576521_1.fastq

Processing SRR6576521_2.fastq

Printing command:
fastqc --outdir SRR6576521_2.fastq

Analysis complete for SRR6576521_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 517M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:41 SRR6576521_1.fastq
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:41 SRR6576521_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:53 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================