-----------------------
Start of variable list:
-----------------------
Sample_ID:
F3-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 19:44:29 EDT 2018
Running on node : scc-yh4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791157
Current job name : Step_02_F3-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/8791157.1.y

Loading required modules...


List files in scratch directory:

total 112M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:44 SRR6575860_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:44 SRR6575860_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575860_1.fastq <==
@SRR6575860.1 1/1
GAATATACAGGCTGTGAATGAAATAATAGCTACTCTTTCCCAGTGTAATGACACCTCATCAGCTGCCATGGTTCAGTGCTTGCGCCAGAAGACAGAGAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575860.2 2/1
TAAGAAAATAAAGCCTAAGGCTCATAGTATAGCTGGAGATCATTTAATATTACCTCCGTGTAGGGTTGCAAGTCAGCTAAATACTTTGACACCGGTAGGA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFF-F
@SRR6575860.3 3/1
TCACATTGGTGGCCTGGGACCCTCGAGGATATGGATATTCCAGACCCCCAGATCGAGATTTTCCACGGGATTTTTTTGAAAGGGATGCAAAGGATGCTGT
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8FFFFFFF-F8FFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFF
@SRR6575860.4 4/1
CAATGATGATGTCAAGTGCTTTTGTTGTGATGGTGGCTTGAGATGTTGGGAACCTGGAGATGACCCCTGGATAGAACACGCCAAATGGTTTCCAAGGTGT
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575860.5 5/1
AAACTGTGTCTTGGTCCAGTTTTTTCACCGCCTCAACTATCTTTCCTTGGGTTCCCTTCTCCACAAAATCATTAATCACATTCTTGGCCTCCTCTGACTC
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFF-F-FFFFFF-F-F-FFFFFFFFFFFFFFFF

==> SRR6575860_2.fastq <==
@SRR6575860.1 1/2
NAGTAGGGTCTGTCTCAGGTGGATTCTTAGCCAGGAGCTCAGTCCAGAAAGCCACTTCCTCTGCTTTCAGTCTCTGGGCTTGCTGGGTAGTGGCTCCAAT
+
#FFFFFFFFFFFFFFFFF-8FFFFF-FFFFFF--FFFFFFFFFFFF-FFFF-F-FFFFF-FF--FFF-FF-FFFFFF-F8FFFFFFFF-FF8F-FF8-F-
@SRR6575860.2 2/2
NTACATGGGAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCA
+
#8FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFF
@SRR6575860.3 3/2
CAGATGCAACCGTGACCCTTTCACATGCTGGAGAAGGAAGTCAGCATGAAAGCGGGGGACCAATGGGTCCTTCTCCCCATGCACAATGAGGGTAGGGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6575860.4 4/2
ATATCATTGACGGTCCTGTAGTTCTCACCAGTGGCCAGGATCTGCCGCTGAACCGTCTGTCTCACCAGGCTCCTACTGAAGCCCATTTCCAAGGCTGCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575860.5 5/2
CCAGTGAGCATTGCCACAGCCTTTGCTATGCTCTCCCTAGGGAGCAAGGGTGACACTCACACGCAGATCCTAGAGGGCCTGCAGTTCAACCTCACACAAA
+
FFFFFFF-FFFFFFFFFFFFF8F8FFFFFFFFF-FFFF-FFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF

Starting FASTQC command


Processing SRR6575860_1.fastq

Printing command:
fastqc --outdir SRR6575860_1.fastq

Analysis complete for SRR6575860_1.fastq

Processing SRR6575860_2.fastq

Printing command:
fastqc --outdir SRR6575860_2.fastq

Analysis complete for SRR6575860_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 607M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 304M Oct 12 19:44 SRR6575860_1.fastq
-rw-r--r--   1 kkarri waxmanlab 304M Oct 12 19:44 SRR6575860_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:55 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================