-----------------------
Start of variable list:
-----------------------
Sample_ID:
C1-MAA100140-3_57_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-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791019
Current job name : Step_02_C1-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791019.1.linga

Loading required modules...


List files in scratch directory:

total 112M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 C1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  55M Oct 12 19:44 SRR6575988_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  58M Oct 12 19:44 SRR6575988_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575988_1.fastq <==
@SRR6575988.1 1/1
AAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACATAGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAG
+
FF-FF8FF-FFFF-FFFFF8FFFFFFFFFFFFFFFFFFFF--F-F-FFFFFFF-FFFFF-FFFFFFFFFFFFFFFF-FFFFF-FFFFF-FF-FFF-FFFF
@SRR6575988.2 2/1
GGGTAATCATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGT
+
FF8FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575988.3 3/1
CTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575988.4 4/1
GTACTTGAACTTCCCATTTTCATTCAGAAAATGCTCAGGTTTAAATGTCTCTGGATCTGGAAACTCATAGTTGTCAAATAAAAGGGAGTCCAGAGTTGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575988.5 5/1
GCACTTTTCCAGAGTGGCTTCATATTTCTTAGCAAGTCTCAGCAACAGGGATACAGAGTAATCAGGGTGTCTTCTTGAATATTAAAACAAGAACGTGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF8FFF-FFFFF-FFFFFF-FFFFFFFFFFFFF-F-FFFFFFFFF-FFFFFFF--F-FFFFFFF--FFFFF

==> SRR6575988_2.fastq <==
@SRR6575988.1 1/2
GCGTAAATCTTAATGCGCCTCTAGAGCTGAAAATCTAGTACCGGCGCAAGACGCAACAGAGCGAAAGCAAAAGCCAAGAAAGATTTCAAAAAACAAGAAC
+
F-------F8FF888-8F-F88F8FF---FFF-F---F-FF-F-F--F-FF-F-F-F--F-F-FFF-FF--F-FFFF-FF-F-FF--FF-FF--FF--F-
@SRR6575988.2 2/2
TCTGCATTCCATCCTGTCTCACTGAGAAGTCCAATTCCAGTCTATCCACATGTTACCTAGGATACCTCATCAAGAATCAAAGACTTCTTTAAATTTCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFF-
@SRR6575988.3 3/2
GGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTACGAGCTTTTTAACTGCAGCAACTTTAATATACGCTATTGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575988.4 4/2
CCTTAAGTCACTGGACATCAACTGCCCCCGGGATGTGACTGACTGTCTCCTCATAGAGATGGAGAAGGAAAAACACAGCCAAGAACCCATGTACACAATG
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFF-F-F--FF
@SRR6575988.5 5/2
GAATGAAGTGCTCCAGTATGCAGAAGTTTGGAGAGAGAGCTTTTAAAGCATGGGCAGTAGCTCGTCTGAGCCAGACATTCCCCAATGCTGACTTTGCAGA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575988_1.fastq

Printing command:
fastqc --outdir SRR6575988_1.fastq

Analysis complete for SRR6575988_1.fastq

Processing SRR6575988_2.fastq

Printing command:
fastqc --outdir SRR6575988_2.fastq

Analysis complete for SRR6575988_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 620M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 C1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 310M Oct 12 19:44 SRR6575988_1.fastq
-rw-r--r--    1 kkarri waxmanlab 310M Oct 12 19:44 SRR6575988_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:24 EDT 2018
0 hours, 0 minutes and 55 seconds elapsed.
==========================================================