-----------------------
Start of variable list:
-----------------------
Sample_ID:
O7-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 19:42:18 EDT 2018
Running on node : scc-ka8
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790890
Current job name : Step_02_O7-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/8790890.1.linga

Loading required modules...


List files in scratch directory:

total 25M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 57 root   root       72K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 O7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:42 SRR6576700_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:42 SRR6576700_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576700_1.fastq <==
@SRR6576700.1 1/1
GTCCCTAAGGATATTATTTCCATTGGAATTCCTTGCTTCTTTTCCATTGCAACAGAAGGTGGGAAACAAGAAACATATTTTTGGAAGGAGAAGAAACCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576700.2 2/1
ACCATCGCAAGAGTAAAAAGGCGCATGTTCAAAAGTTATAAACTTGGAAAAGCAGGTTTGACTTACAACGATAATACAGAATGGAATGACTATTCCACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576700.3 3/1
TCCTTTGGGAGAAATGTAAACATCCATCTAATCTGTCAGGACTTTATGAGACCTTCCAAGAATACAAAGCATTTCTCTCATTGCCTCAAATGACTTGAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576700.4 4/1
TGCTGACTCACCTTCCCAACCCTCAGATTAAAATGTTACAGACAATTCTAAACTAAGGTACTTCGATAGCTGGCTTTCACTGTCATCTTGATAAAACCCA
+
-FFFFFFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFF-F-FFFF-FFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576700.5 5/1
CCACTCATTCATTGACCTACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCCTTCTAGGAGTCTGCCTAATAGTCCAAATCATTACAGGT
+
F8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576700_2.fastq <==
@SRR6576700.1 1/2
NGAATGCGAAGCCCTGAACAGCGAAACTTGACTTCCTGGAGCACTTCAGACAGGTGTATTCATTTCCGTGTTCTGCAAGCAACCATTTAGTCCCCAGCAG
+
#F-FFFFFFFFFF8FFFFF8F8FFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFF-FFFFF-FF---FFFF--FF-FFFF8-FF-F-FF
@SRR6576700.2 2/2
GGTGGTGACACCATCCAGCCGGTGACCATGTTCGACAAGACGCGGCTGCCGTACGTGGCCCTCGATGTGATTTGCGTGTTGCTGGCTGGATTGCCTTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576700.3 3/2
CGTTGACAGTGGGCAACTCAGGTAACAAAACTGCTCTGGTCACCAGAGGCTTTTCCATGACTCCTGATTCCTACATGTAAATAGTCTCTCATACACTTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576700.4 4/2
ATTTTACTGTCTGGGGAAACCTGGGGTGAACACTGTAAATTCCTAGGCTGAGCGACCTGTCGGCTGCTGTGATAAATACCCTCATGAAAGGCAGCGCAGG
+
F---FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FF-FFFFFF-FFFFFFFFF-F-FFFFFFFFFFFFFFF-FFFF8FFFFFFFFFFFF-FF-F-F8
@SRR6576700.5 5/2
GAATTAAGACTATGATTAGGATACCTAGGATATCTTTGATTGTATAGTAGGGGTGAAATGGAATTTTATCTGCATCTGAGTTTAATCCTGTTGGGTTGTT
+
FFFFFFFFF8FFFFFFF-FFFFFFFFFFFFFFF-FFF-FFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFF--FFFFFFFFF-FFFFFFF-FFFFFFFFFF

Starting FASTQC command


Processing SRR6576700_1.fastq

Printing command:
fastqc --outdir SRR6576700_1.fastq

Analysis complete for SRR6576700_1.fastq

Processing SRR6576700_2.fastq

Printing command:
fastqc --outdir SRR6576700_2.fastq

Analysis complete for SRR6576700_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 127M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 57 root   root       72K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 O7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  64M Oct 12 19:42 SRR6576700_1.fastq
-rw-r--r--   1 kkarri waxmanlab  64M Oct 12 19:42 SRR6576700_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:38 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================