-----------------------
Start of variable list:
-----------------------
Sample_ID:
C18-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 19:41:27 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790740
Current job name : Step_02_C18-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/8790740.1.linga

Loading required modules...


List files in scratch directory:

total 24M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576935_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576935_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576935_1.fastq <==
@SRR6576935.1 1/1
GCCCTCACTCACGGGGCTAGACATGAACATTGACCCTGACTCCATCATTGCCTCTTGTACACCAGGCGCTGCCGTCAGCGTGGTCACGGCAGAAGTTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576935.2 2/1
GTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGG
+
8F8FF8FFFF8FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576935.3 3/1
GTACATGGGGGAGAAGGGGAGACAAGCTGAAGGAGAGAGCAATCAAGATGACGGAGAAGGATGCACAGCCACAGCTGGAAGAGGCGGACGACGACCTGGA
+
F-FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576935.4 4/1
GTTCAACATAGTATGGAGATGACCTTGGTTGATTTCTTTTTGTTGACAATGAAGTTTGACCCATTAGTCTCTGCCTTTGTGAGAAACAAAGGAAACAAAG
+
FFFFFFFFFFFFFFFFFFFFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576935.5 5/1
GTCTGAGAGAAAGAGTTTGAGAGGTGGGGAGGACCTTAGAGTCCCAGCCTTTGCCTCTCAACACCTCAAACACATTGACAAGTAGTTCCGAACAATGTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF

==> SRR6576935_2.fastq <==
@SRR6576935.1 1/2
GCCTTGGTCATGATGTTTTTATCAGAGCAATAACAAAGTATCTAAGACCACCAGATCCCAGGAAGCTGTATTTGCTTGGTTCTCCCATGCCTCCTCTCAG
+
FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576935.2 2/2
TTTTTTCTCACGGTACTGGTTCACTATCGGTCAGTCAGGAGTATTTAGCCTTGGAGGATGGTCCCCCCATATTCAGACAGGATACCACGTGTCCCGCCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF8FFFFFF8F8FFFF
@SRR6576935.3 3/2
GTCCAATCCTTCTTAATGGCCAGGTTCCATTCCCAGGTGAGGTGGTCCTGTTTGTCGTCATCCGTGAAGAAGGACTTGTTGTGGTAAGTGCCTCGGGCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-F-FFFFFFFFFFFFFFF-FFFFFFFF-FFFFF--FFFFFFFFFFFFFFF8FFFFF-F8FFF
@SRR6576935.4 4/2
TGCCTCTACCTCCCTAGTACTGGGATTACAAGCAGAGCTGCTGTGCCTGGTTTATGTAGTACTGAACCCAGGGCTTCATGCATGCCCTCTATTAACTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFF8FF-FFFFFFFFF
@SRR6576935.5 5/2
GCTGGGAAGTTGCTGTACAGAACACTGCCGTGTGGGAAAGGCCCAGCAGCCTCCTGCTCCTCCTCTCTCCTTACAGAGCAACAGGGCTTTTTCTTGTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576935_1.fastq

Printing command:
fastqc --outdir SRR6576935_1.fastq

Analysis complete for SRR6576935_1.fastq

Processing SRR6576935_2.fastq

Printing command:
fastqc --outdir SRR6576935_2.fastq

Analysis complete for SRR6576935_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 119M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root      112K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:41 SRR6576935_1.fastq
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:41 SRR6576935_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:52 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================