-----------------------
Start of variable list:
-----------------------
Sample_ID:
G19-MAA000377-3_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 19:49:49 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791377
Current job name : Step_02_G19-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791377.1.linga

Loading required modules...


List files in scratch directory:

total 42M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 100 root   root       84K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 G19-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  20M Oct 12 19:49 SRR6576236_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  22M Oct 12 19:49 SRR6576236_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576236_1.fastq <==
@SRR6576236.1 1/1
GNTCTGGGACACAGCCGGTCAAGAACGGTTCCAGTCTCTTGGTGTGGCCTTCTACAGAGGTGCAGATTGCTGTGTTCTGGTGTTTGATGTGACTGCCCCC
+
8#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576236.2 2/1
GTACATGGGGACCCGGGAAGTGTCCCTGTCCGTGGCCTCTGCAGCCTCCCGCTTCCCGGCACCATGGAGTACCTCATTGGCATCCAGGGCCCAGACTATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576236.3 3/1
TCTCTCTGCAGCACAATGCACTATGACATGAGGCTGGAAATCATGAATGAGGTGATGAACAGCTTCAGAATCCAACAGGTTCACTTGTTCGAATTTTGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576236.4 4/1
CACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGTGTCAAATTAAGCCGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576236.5 5/1
GGTCTGATCTTTCTGGGTTTTGAGACATGGTTTCAGGGTTTTACTGTCTGGCTGTCCTCGAACTCTATTTGTAGACCAGACTGGCCTTGAATTTAGATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576236_2.fastq <==
@SRR6576236.1 1/2
NCTCAGAACGGAGCCTGGGCACCAGCCTTCCCACAGGACCTTCAAGGAGGGAGGGGTAAAAGACCACAATACCGTTAAAAAAAAAAACAGATAAATTGAC
+
#-FFFFFFFFFFFF8FFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFF-FFF-F-FF-FFFFFFFFF-F----FFFFFFFFFFF-FF-FF8F-F--F-
@SRR6576236.2 2/2
TGGTAGGTGTGTAGTATCGGTCAAGGATGCTGAGAGTCAGAAAGGCACCATAGCCATGAGCTGCAAAAGGAGCCTTAGCCAAGGCTGCCAGGTAGTCCAT
+
FFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576236.3 3/2
CGTGTGCTCCGTGCGGGCGGAGCGAACAAAGACCGGGCCAGAGGAGCCAGACGCCCAGATCCCTCTCGCTGCGTTTCCCCAAAATAGTTCTGGAATCATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF
@SRR6576236.4 4/2
TCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGG
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFF
@SRR6576236.5 5/2
GACTCAGAGAGGTCACCCACTCACCCAGTCTCACAGCCTTTAAAGATCAGAACCTTACCCAGGCGAGGTTATGCCTTTCATCCCAGCAGGGGCAGGGACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576236_1.fastq

Printing command:
fastqc --outdir SRR6576236_1.fastq

Analysis complete for SRR6576236_1.fastq

Processing SRR6576236_2.fastq

Printing command:
fastqc --outdir SRR6576236_2.fastq

Analysis complete for SRR6576236_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 217M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 100 root   root       84K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 G19-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 109M Oct 12 19:49 SRR6576236_1.fastq
-rw-r--r--    1 kkarri waxmanlab 109M Oct 12 19:49 SRR6576236_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:16 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================