-----------------------
Start of variable list:
-----------------------
Sample_ID:
D7-MAA100138-3_56_F-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 19:44:30 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791090
Current job name : Step_02_D7-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791090.1.linga

Loading required modules...


List files in scratch directory:

total 57M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6575816_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:44 SRR6575816_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575816_1.fastq <==
@SRR6575816.1 1/1
GCGGAGGAATTGGGGCAAGAGGTCCCGGGGAAACGAAACTGGAAACCGACCGCCGCCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFF-FFFFF
@SRR6575816.2 2/1
GTCCATAATTGCTGGAATACTCATACAGAAACTGGTCAGCAAATCCCTTTGGGTCCCTCCTGAAGGCCTCACAGATCTCATCATTTGTTGGTTCCACGTA
+
FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F--FFFFFFFFFFF-
@SRR6575816.3 3/1
TCTTTCTTCTTTCACGGTATCGGCTTCTATGGCGAATGACAGTGGAAAGCTGTGTGTTGATTTCATGAATGCGATTTCTGATATGGCGGCGGTCGGTTTC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575816.4 4/1
CTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAAC
+
-F8FFF-FFFFFFFF-FFFFFFFF8FFFFF8FF8FFF8FF-F8-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFF--FFF-FFFFF-FF-FF-FF
@SRR6575816.5 5/1
GCATCGGAAGACACTTCGTGCCGACACGAAGCAGCCTCAATATCTAACACGAGGATGTTCCTGTTGATACCGTCTGCGATAGGCTAGTTCATAATCGAGG
+
F8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF

==> SRR6575816_2.fastq <==
@SRR6575816.1 1/2
ATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCACTGTTTTTTTCATTTCCCGCATAATCCTCATTTGAAGAATCAATTAAATCCAGAATTAAATCCGA
+
FF-FFFFFFFFFFFFFFFFFFFFFF--FFFFFFF--FFFFFFFFFFFF-F-F-FFFFFFF-FFFFF-FFFFFFF-FFFF-F-FF-FFFFFFF--FFF-F-
@SRR6575816.2 2/2
ACCAGGACCTCAGAGCTGTCTGTTAAGTCCTGTGAAAGTGATGCTCCCTTTCCGGTTCACCCTGGAACTCCTGAGTGTTGCACCAAGGAGGGGCTGGAGC
+
FFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFF--FFFFFFFFFF-FFFFFF-FFFFFFFFFFF-FFFFFF8FFFFFF--FFFFFFFFFFFF
@SRR6575816.3 3/2
CTTCAAATTGAGCTGGCTCAGCTGCAATATGCACTGCCGCGTCTGACGGGACAAGGGATCAACCTTTCCCGGCAAGGCGGAGGAATTGGGGCAAGAGGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFF8FFFF8FFF
@SRR6575816.4 4/2
TGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCACCGTCACCCGTTGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATA
+
FFFFFFFFFFFF8FFF8-FF8FFFFFFFF-FF--FFFF-FFF-FFF--FFFFF---FF-FFF-FFF--FFF-FFFFFF-8FFFFF-FFF-FFFFFFF-88
@SRR6575816.5 5/2
AACATGCACAGCGGTCAAACAGTATGTCCCAAGGGGACTTAAGCGCGGTGGCCTCCCCTATCCCCTACGAGGCTACCCGGATCGATGACGCGAATTGGGG
+
F--F-FFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFF-FF-F-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFF8F--8FFFF

Starting FASTQC command


Processing SRR6575816_1.fastq

Printing command:
fastqc --outdir SRR6575816_1.fastq

Analysis complete for SRR6575816_1.fastq

Processing SRR6575816_2.fastq

Printing command:
fastqc --outdir SRR6575816_2.fastq

Analysis complete for SRR6575816_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 298M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 149M Oct 12 19:44 SRR6575816_1.fastq
-rw-r--r--   1 kkarri waxmanlab 149M Oct 12 19:44 SRR6575816_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:05 EDT 2018
0 hours, 0 minutes and 35 seconds elapsed.
==========================================================