-----------------------
Start of variable list:
-----------------------
Sample_ID:
A10-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 19:42:18 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790909
Current job name : Step_02_A10-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/8790909.1.linga

Loading required modules...


List files in scratch directory:

total 47M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A10-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:42 SRR6575324_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:42 SRR6575324_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575324_1.fastq <==
@SRR6575324.1 1/1
TNACAGCACAGAGCTGGTAGGGGTAGGGGGCAACCGGAAAAGGAAAGACACCAAGGTTTCTAGGCCTGGGCTGTCCATTGGNCACTGAGAAGCTAAAGTG
+
F#8FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFF-FFF#FFFFFFFFFFFFFFFFFF
@SRR6575324.2 2/1
TCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCATCCTTTTCGTTAA
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575324.3 3/1
GACTATGACCCTGGTCTTGAAGGCCATAGGCAATATCTTCCCACAGGTCGTCCAGTCGGCTCTGCAGTCTGCTCAGGGCCTTATTACTGTCTGAGTGTCC
+
FFFFFF--FFFFFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575324.4 4/1
CATAAGAGCCCTGGCCCAAGGTCAGGCCCTTCCCAGCCAGACCGGCCTCAGTAGAATCGTTTGTTCCGTTCCTGGCGCTTCTGAAACACCACTGCGCCCA
+
FFFF--FFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFF-FFFFF--FFFFF-F--FFF--FF-FFFFFF-F-F-FFFFFFFFFF-FF-FFFFFFF
@SRR6575324.5 5/1
CCCAGTGCCTCAGCCCGGCTCTGCCACTTGTGGAGACCCTCTCCATGCTCTCTCTTAGGCTCCAGCTGTGCACATCTGTGCAGTCAAGGCCTCCTCCCCA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFF

==> SRR6575324_2.fastq <==
@SRR6575324.1 1/2
NTCATNGGGCAGGNGCGGCATCCAGAGATGACAGACCAGGCTCGTATGCCCTACACCAATGCTGTCATTCATGAGGTACAGCGCTTTGGGGACATTGCTC
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8FFFF8FFF
@SRR6575324.2 2/2
GCAAATCCGTGTCTTGGAGAATTCCTTAGTTCTTAAATTCCATACTGTAAGAGATGAAGAGTGCTCGGAATTATCTATGGTTGCTGACAAAACAGAAAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575324.3 3/2
CTGTCCCACAAACTCACACGTAAGGCGAAGGACCTGCACACCAGCATCCAACGCAACCTGGACCAGCTGCGCGATGAGCTCAGTGCCTTCATCCGCGTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575324.4 4/2
ATCAACGCAGAGTACATGGGACGGTGATGACTGACCTGGAAGACAAGAACGAGTGGAAGAACTGCATTGACATCACAGGGGTGCGCCTGCCCACTGGCTA
+
FFFFFFFFFFFF8FFF8FFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-
@SRR6575324.5 5/2
GTCCTGGGGATATGGACTAGGTTTCTATTCCCAAAAGCTACAGTGACTTTGATGGTCCCTGGTCAAACGTGCGAGATCTTGACAATATACATTTAGTAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF8FFF

Starting FASTQC command


Processing SRR6575324_1.fastq

Printing command:
fastqc --outdir SRR6575324_1.fastq

Analysis complete for SRR6575324_1.fastq

Processing SRR6575324_2.fastq

Printing command:
fastqc --outdir SRR6575324_2.fastq

Analysis complete for SRR6575324_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 261M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A10-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:42 SRR6575324_1.fastq
-rw-r--r--   1 kkarri waxmanlab 131M Oct 12 19:42 SRR6575324_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:49 EDT 2018
0 hours, 0 minutes and 31 seconds elapsed.
==========================================================