-----------------------
Start of variable list:
-----------------------
Sample_ID:
E5-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-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791122
Current job name : Step_02_E5-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/8791122.1.linga

Loading required modules...


List files in scratch directory:

total 80M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:44 SRR6575838_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:44 SRR6575838_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575838_1.fastq <==
@SRR6575838.1 1/1
CTCCTGTGGTCTGACCCTGACAAGGATGTTCAAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575838.2 2/1
GGCCATGAAGGGTCAGCGGCTGCTGGACGTGGCAGAGCTGGGGTCCCTGTGAGGATGATGGCTGGGGTGCTGGCCAAGGGCACCCCGCTCGCCACTGAGC
+
FF-FFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575838.3 3/1
CCTTTAAAGAGAATGTAATTTGCCAGGGCGAAAACTGTGTCTTGGTCCAGTTTTTTCACCGCCTCAGCTATCTTTCCTTGGGTTCCCTTCTCCACAAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575838.4 4/1
TATCAACGCAGAGTACATGGACCAGCCCCAAACCAAGAGACAGGAGGCAGCTCCTGGATCCGCCAAGCGACCTGAGCAGGGCTACCCACTTGGAAAAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575838.5 5/1
GTTCTGATCTTCATGGCCCTGCATCCGGTTCCCACATGTCTCAGGTGGCCGCCCACACAGCGGTCACAGTTGGACGGAAGTCCGTCCCTGACCATGGTCC
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575838_2.fastq <==
@SRR6575838.1 1/2
AGGAAAGACACTTAACGCTGTGTGTTCCCCGTGACGGGTGGGCCTGAGAGGCCAGTGTGACCCATGGCAGCATGATTTCTGTACAAACGATCTGGGGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575838.2 2/2
GGAAGAGTGAGAGGTGGAAGAGTTGTGGCGAGTGGAGAGGACCCAGAGAGGGAGTCCGAGAATAGCATTCCTGGCTGAGGGAATGAGGAATCTGCACACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575838.3 3/2
CTGCAGCTGAGCACAGGCAATGGCCTCTTTGTCAACAATGACCTGAAGCTGGTGGAGAAGTTTCTGGAAGAGGCCAAGAACCATTATCAGGCAGAAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575838.4 4/2
ATTCAAAAATGGCCTCACTGTAGCCCAAGCTCACAGCGGCCATGGGTGGCGCTCCATGCCACAAGGCTGGGATGTGCCAGACGTGCTGCCTCTCGGCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6575838.5 5/2
GAGGAGTATGAGCTCAACGGCGACCTGCGCCCGGGCTCCCCCGGTTCCTCCGACGCCTTGCCACCCCGCTGGGGTTTGCGGAACCGGCCCATCAATGTAA
+
8FF---FFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFF--FFFF-FFFF--F-FFF-FFFFFFFFFFFFF-FFF---FFFFFFFF-FFFFFFFF-FFFFF

Starting FASTQC command


Processing SRR6575838_1.fastq

Printing command:
fastqc --outdir SRR6575838_1.fastq

Analysis complete for SRR6575838_1.fastq

Processing SRR6575838_2.fastq

Printing command:
fastqc --outdir SRR6575838_2.fastq

Analysis complete for SRR6575838_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 442M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 221M Oct 12 19:44 SRR6575838_1.fastq
-rw-r--r--   1 kkarri waxmanlab 221M Oct 12 19:44 SRR6575838_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:57 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================