-----------------------
Start of variable list:
-----------------------
Sample_ID:
F2-MAA000907-3_11_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 19:41:27 EDT 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790779
Current job name : Step_02_F2-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790779.1.linga

Loading required modules...


List files in scratch directory:

total 27M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576310_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576310_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576310_1.fastq <==
@SRR6576310.1 1/1
GNGGTGATAAGAGAACCAGGACGGGTGATGATAAGAGAGGGTGTGCATGGGAGCATTTACTCTCTGTTCAGTTTTTAATTANCTTAAATGTGCTATAAAA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFF-FFFFF
@SRR6576310.2 2/1
GTACTCACAGTGACTTCGGAACCTAACCCCTGCTGTTCTTGAGGAGAGATGAACAGCTCAGGCCTCTCGTTCCCAAATGGCCTTTTGCCATTTAGTGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF--F-FFFFF
@SRR6576310.3 3/1
CCACAAGGAGGTGGAAACCTTCTCCCATGTCTCTCTGTCAGACTTACTGACAGAGAGACATGGGTTAGGTTCCACAAGGAGGTGGAAACCATCTCCTTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576310.4 4/1
GTTCTAAAAGTTTCAACATTAAGCTTGGAGCAGAGATGGACAGCCTCGGTGGCAAATGTGATCCCAGTCAGCAGAAATTCTGTGATGGACCGCTGAAGCC
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576310.5 5/1
GCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACCATTTTATAATATAATAAAAAAATTTATTGATAATTTTATTTAAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-----FFF-----F------FF----F-------F-FF----F--FFFF

==> SRR6576310_2.fastq <==
@SRR6576310.1 1/2
NCCTANGGCCAGTGAGATGGCCAAGTGGGTAAAGGCAGATGCTGCCAAGCCTGAAGCCTGCTCAAGCCCTGACCCAAGGTGAGAACCCACTCTCCCAAGT
+
#FFF-#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF8FFFFFF8FFFFFFFF
@SRR6576310.2 2/2
GATTAAAGGCATGCACCACACCCTGAGTAAGAAAGTTTGCCTGTATGTATGTCAGTGCATCACAAGCATGCAGACCCAAAGGGGCCAGAACAGGGCAACA
+
FF-FFFF-F8FFFFFFFFFFFFF8FFF-F--FF-F----FF---FFFF----F--F-FFFF-FFF-F--FF-FFFFFF-FF--FF-FFFF-FFF8FF-8-
@SRR6576310.3 3/2
GTATCAACGCAGAGTACATGGGACTCTGCTATATTCTTTAAGCTTCTTTGCTTCCTCATAACCTGATCCCAGGGACATGAGCTTGTTGGAAATCATAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576310.4 4/2
ACTGGCTTCTACCCACGTCTTTTAAGTCCTCATATTCCTTGGATAGAAGGTAGTTGGAGTCTGCCTGCAGCTTCATGAAATGCCCTTCAAACTTATTGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF--FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF--F--FFFFF
@SRR6576310.5 5/2
CTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTTGTTGGTTTATGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576310_1.fastq

Printing command:
fastqc --outdir SRR6576310_1.fastq

Analysis complete for SRR6576310_1.fastq

Processing SRR6576310_2.fastq

Printing command:
fastqc --outdir SRR6576310_2.fastq

Analysis complete for SRR6576310_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 137M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  69M Oct 12 19:41 SRR6576310_1.fastq
-rw-r--r--   1 kkarri waxmanlab  69M Oct 12 19:41 SRR6576310_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:42 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================