-----------------------
Start of variable list:
-----------------------
Sample_ID:
C12-MAA100041-3_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 19:44:28 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791010
Current job name : Step_02_C12-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791010.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C12-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6575383_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6575383_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575383_1.fastq <==
@SRR6575383.1 1/1
GACCTGGGCTTGTGACAGGAACCATCAACTATACAGAAGTGACAGGCCTTTTCCTCTTTGTTTTTCCAGCCCCTTTCAGTCTGTCACTTGTCCTTTCTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575383.2 2/1
GTATGGAACCATCTGAAGCAATCTCTCCAACTTCTAGGTCTAACGAGGACTTATTTGCAACAGTACAGAAGGGAGTCAGAGTGACTACTCGTGAGAGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575383.3 3/1
TTCCTAACTTCTCCACACAGTAGACGGCCTGACTTGCAAAGGCCTCATTGATCTCAAAGATGTCTATGTCATTCACAGTCAGCCCTGCTTTCTGCAAGGC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575383.4 4/1
GTTAAGAGCTGAGCACACAGGTTCTCTCTGAATTGGGTCAAGCTGATTTCCAACTGGACTATTCCAAGGATCCGAATATGCTAGTAAGCTGAATGCGTCC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575383.5 5/1
CCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6575383_2.fastq <==
@SRR6575383.1 1/2
CTCCCACACAGCCCTCCCCTTACACCCTCTGGGGCTGGTCACTCTGTCTTTGACCTCTGCTGTATCCCTCATACTGTTCCAGGTGTGGAGGGGGAATGGA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFFFF-FFFF
@SRR6575383.2 2/2
ATACAGCTTTTACTAGTTACTTATCTAAGACTCCTAGTTTATATATTCTCAGTTGCACGTGTGTGACCTATGTCTTCATTTTTGACACTGAATAAAGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575383.3 3/2
CAAGGATGGAGGCTCTACCACGGCTGGAAACTCCAGTCAGGTGAGTGATGGAGCAGCTGCCGTCCTGCTGGCTCGGAGGTCCAAGGCTGAAGAACTGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575383.4 4/2
CATGGAAACAGATCACTACTCCAATGGAGTTGGAGAAACTTCATCCAATGGTTTCCTAAATGGTAGCTCTAAACATGACCACGAAATGGAAGATTGTGAC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF-8F-FFFFFF
@SRR6575383.5 5/2
ATCAACGCAGAGTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAG
+
FFF-FFFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF

Starting FASTQC command


Processing SRR6575383_1.fastq

Printing command:
fastqc --outdir SRR6575383_1.fastq

Analysis complete for SRR6575383_1.fastq

Processing SRR6575383_2.fastq

Printing command:
fastqc --outdir SRR6575383_2.fastq

Analysis complete for SRR6575383_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 318M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C12-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 159M Oct 12 19:44 SRR6575383_1.fastq
-rw-r--r--   1 kkarri waxmanlab 159M Oct 12 19:44 SRR6575383_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:04 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================