-----------------------
Start of variable list:
-----------------------
Sample_ID:
K7-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 19:41:26 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790701
Current job name : Step_02_K7-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/8790701.1.linga

Loading required modules...


List files in scratch directory:

total 25M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 80 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576517_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576517_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576517_1.fastq <==
@SRR6576517.1 1/1
CTGCATACATAGTCGAAAGGCCTAGCACTGCAAAGGACAAGCACAAGGAAGAAGACAAAGGCTCTGATAGAATAACAGTGAAGAAAGAAGTGCAGTCACC
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576517.2 2/1
GTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTC
+
F-8FFF-FFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFF---FFFFFFF--FFFFFFFFFFFFFFF-FFFFF--FFFFFFFFFF----FFF
@SRR6576517.3 3/1
CACAAAGAAGTGGGACTTCTGGGCCACAAGATCCACCATCTTTTGTATGTGAGCTCATTAACCCTTTTGAAGACTTCTAACCAGAGGAAGGTAACCATTC
+
FFF8FFFFFFF-FFFF-FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-F-F-FFFF-FFFFFF-FFFFF-FF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576517.4 4/1
GCAGTGTGCAGGACCCGGAACTCTCTCAGGGCAGCTACTTTGTCCACAGGTTCAGGTTTCTGATCAGGCTCAGGCCAAGATTTTCGGAGAACATGGACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576517.5 5/1
TGCTGGAGGAGGGCCTCGAGGTCCTTTCTGACTCCTGTGACGGATGAAAAGGCCAAGCCCGAGGAAGATCACCCCAAGCACGCAGCCCCCGATGCCGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576517_2.fastq <==
@SRR6576517.1 1/2
NGCTTCCTCAGAGCGCTGGGAGAGATGTCAATCCTCCTGTGTATCTCGGGGCTCTTTTGCCGGGTACTATGTTCTTCAGTAGCTTTCTGGTATGAAGTGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFF-FFFFFFFF-FFFFFFFFFFFFFFFFF-FFFF-FFFF8FF-F-FFFFFF-FFFFFFFF
@SRR6576517.2 2/2
ACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576517.3 3/2
AAAATAATGAGAGGAAGAAATGAGACCATAGAACAAATGTAGAGTACTGGAGAGAAGGACCAATCGGGTCTCTTAAATCTCCATTAATGGTCCTATGGGT
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFF-FFFFFFFFFFFFFFFFFFFFF-FFFF-FFF--FFFFFFFF-FFFF-FFFF-FFFFFFF
@SRR6576517.4 4/2
GACCAGAGGAGAAAGAGAGAGCGCGAAAGAGAGAGGATGTCTCTCTCAGACTGGCATCTGGCAGTGAAGCTGGCTGACCAGCCACTTGCTCCAAAATCTA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576517.5 5/2
GCCAAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGTGGGGGTCTCATCCACACAGCTTATTAGGAATGGGGACTGGACCTTCCAGGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF

Starting FASTQC command


Processing SRR6576517_1.fastq

Printing command:
fastqc --outdir SRR6576517_1.fastq

Analysis complete for SRR6576517_1.fastq

Processing SRR6576517_2.fastq

Printing command:
fastqc --outdir SRR6576517_2.fastq

Analysis complete for SRR6576517_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 129M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:41 SRR6576517_1.fastq
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:41 SRR6576517_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:50 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================