-----------------------
Start of variable list:
-----------------------
Sample_ID:
H6-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 19:46:09 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791248
Current job name : Step_02_H6-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/8791248.1.linga

Loading required modules...


List files in scratch directory:

total 36M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 37 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:46 SRR6576399_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:46 SRR6576399_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576399_1.fastq <==
@SRR6576399.1 1/1
GTGGGGAAGAGGTGGTGCTCAATCTGGAAATTGAGGTGCCCGCTGAACCAGTCATTGAAGAAGGACTGCTCCACATTGCAGGTGGCTGCCAGCTGGCTGC
+
F-FFFFFFFFFFFFFFFFFFF88FFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFF--FFFFF
@SRR6576399.2 2/1
GTACATGGGGGAGTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-
@SRR6576399.3 3/1
GTCCTGAGCAGAGAGCTGAGCAGAGTGTCGGTGGGCAGGGGGCTCAGGTAGCCAGGAAGCCCCCATCCACTGGCAAAGTGGAGCCAGTGGTCATGCCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576399.4 4/1
GTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCAGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576399.5 5/1
CTACCAGGACCAAGAGGTACCCAAGCCAGAATACTGGGGTGGCTACATCCTGTACCCCCAAGTGATGGAGTTTTGGCAAGGCCAAACCAACCGCCTCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576399_2.fastq <==
@SRR6576399.1 1/2
CCCACCTTCCGTACGGAGGAGAAACATAAGCACAACCAGCGCACCGCCCGCTGACTCGTCATCGACCGAAAGGACAACAACCTTACCAAATGGTCCCAGC
+
---F--FFFFFFF88-F-FF8F-FFF-FF-FFFF--F--F-FFFFF-F---F--F--F-FF-F-F----F-F-FF-FFFFF--FF-FF-FF--F8--8--
@SRR6576399.2 2/2
ACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTCAGGATTCCATGCTTCTCAC
+
-FFF-FFFFFFFFFFFFFFFFFFFFFF-FFFF-F-F-FFFF--FFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFF
@SRR6576399.3 3/2
GTAGTGATGACACCCATGGGCCGGACCAACTGGAGTGACCCCCACAAAGCTAAGGCCATGCTGGATCGTCTCCCACTGGGCAAGTTCGCTGAGGTGGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFF--FFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576399.4 4/2
GGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGA
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFFFFFFFFFFFFFFFF---FFFFFF-FFF-FFFFFFFFFFFFF-FFFFFFFFFF8
@SRR6576399.5 5/2
TCTCCAAACAGCTCAGGGGCCAGCAACTTAGTCTTAAAATAAAAGGTAAAGAGAGAGAAATGCTGGGACTCTCACTCAGTGGTACAGAGTTGCCGAGCCT
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF

Starting FASTQC command


Processing SRR6576399_1.fastq

Printing command:
fastqc --outdir SRR6576399_1.fastq

Analysis complete for SRR6576399_1.fastq

Processing SRR6576399_2.fastq

Printing command:
fastqc --outdir SRR6576399_2.fastq

Analysis complete for SRR6576399_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 202M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 37 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 101M Oct 12 19:46 SRR6576399_1.fastq
-rw-r--r--   1 kkarri waxmanlab 101M Oct 12 19:46 SRR6576399_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:27 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================