-----------------------
Start of variable list:
-----------------------
Sample_ID:
C7-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-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791039
Current job name : Step_02_C7-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/8791039.1.linga

Loading required modules...


List files in scratch directory:

total 65M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 C7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  32M Oct 12 19:44 SRR6575788_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  33M Oct 12 19:44 SRR6575788_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575788_1.fastq <==
@SRR6575788.1 1/1
ANAGAGGGGCGTTGAGTCCGTCCGACTTCACTGCCCCCTTTCAGCCTTTTGGGTCCTGTATCCCAATTCTCAGAGGTCCCGCCGTACGCTGAGGACCACC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575788.2 2/1
CGTATAGGAAAAGTCAGACTACGTCTACAAAATGTCAGTATCATGCTGCGGCTTCAATTCCGAAGTGATGTTTTGATGTGAAGTGAAATTTTAGTTGTCG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFF-FF-FFF-FFFFFFFFFFFFF-FFFF-FFFFFFFF
@SRR6575788.3 3/1
CGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575788.4 4/1
GTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575788.5 5/1
GGGCGGCCCCCTTTCCGGCCGCACCCCGTTTCCCAAGACGAACGGCTCTCCGCACCGGACCCCGGTCCCGACGCCCGGCGGGGGGAGACCCCGCGCCGCC
+
FFF8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575788_2.fastq <==
@SRR6575788.1 1/2
NACATATGCAGATCCCCTGAGACAGAGTCGCTATCGTTATGTCTCCTTCCCGCGGTCAAGGCGAAACCGCAGCAAACTTCCTCAGACGCTGCCCGAACTG
+
#FFFFFFFFFF-FFFFFFFFFFFFFFFFFFF--FFF---FF---FF-F-FFF-FF-F-FFF-FFF-FFFFFFF-F-FF--F-F-F--F--F-FF---8-F
@SRR6575788.2 2/2
NCATTATACTAGGACTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFF--F
@SRR6575788.3 3/2
GTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575788.4 4/2
GGTATCAACGCAGAGTACATGGGATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTACTATAC
+
FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575788.5 5/2
AAGCTACCATCTGTGGGATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCGGAACGATACGGCAGCGCCGAAGGAGCCTCGGTTGGCCCCGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575788_1.fastq

Printing command:
fastqc --outdir SRR6575788_1.fastq

Analysis complete for SRR6575788_1.fastq

Processing SRR6575788_2.fastq

Printing command:
fastqc --outdir SRR6575788_2.fastq

Analysis complete for SRR6575788_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 369M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 C7-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 185M Oct 12 19:44 SRR6575788_1.fastq
-rw-r--r--    1 kkarri waxmanlab 185M Oct 12 19:44 SRR6575788_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:08 EDT 2018
0 hours, 0 minutes and 38 seconds elapsed.
==========================================================