-----------------------
Start of variable list:
-----------------------
Sample_ID:
H16-MAA000377-3_9_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 19:46:10 EDT 2018
Running on node : scc-yf4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791327
Current job name : Step_02_H16-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791327.1.y

Loading required modules...


List files in scratch directory:

total 16M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H16-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 7.6M Oct 12 19:46 SRR6576292_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 8.1M Oct 12 19:46 SRR6576292_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576292_1.fastq <==
@SRR6576292.1 1/1
GAATTAGAAGTGGGAAAAGAATGCAGCCAAGCACGTCTGTTCTGAAGCTACTGGGGTGGTTTCTCATGCTTCAGAGTCTCATATGTCTCCTGGCTCCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576292.2 2/1
GTAAACACGCGGCCCCCAGTCGGCAGGCTCGCCACCGTCGGCGTGCGGCAGGTGGTCCCGGCTGCCTTCGCCGGTCGGGCCGGGAATGGGGCGGGTCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576292.3 3/1
TCTCTGCCCTGAGGACCATCAACAGCCCCTTGCGACCGAACCAGGTCATTCGCTTCGAAAAGGTGATCACCAACGCGAACGAGAACTATGAGCCACGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576292.4 4/1
GTAAACACGCGGCCCCCAGTCGGCAGGCTCGCCACCGTCGGCGTGCGGCAGGTGGTCCCGGCTGCCTTCGCCGGTCGGGCCGGGAATGGGGCGGGTCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576292.5 5/1
GTCCTGGGTCATGTTGCCGTACTTGGTAACGTTCTTCACAGGCCCAAGGAGCATGTTATCCATGGACATTGGACGCATCAGCAAGGGAGTAGCCATCCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576292_2.fastq <==
@SRR6576292.1 1/2
GGATGATCTCAGCCGTGATCTTGTTCTTGCTCCTTTTGGTGGAACAAGCAGCCGCCCTGGGAGAGCCGCAGCTCTGCTATATCCTGGATGCTGTCCTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF
@SRR6576292.2 2/2
CTGCTCGCGGTTGCCGTCGGGCGGCAGGTTGCCGCGCACGAACACGGTGGACTCCAGCAGCATGCGATAGAAGGCGGGACGCGCTTCCGGGTCTTCGTGG
+
FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576292.3 3/2
GTTGGATAGGTGTAATTTGACCCCGTGATTACGCATCCATGTCAGGGAAAAGCAGAAAGCCAGTGAAGATGCTGTTGGCACCCTCAATGCCCAGGAGGGA
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576292.4 4/2
CTGCTCGCGGTTGCCGTCGGGCGGCAGGTTGCCGCGCACGAACACGGTGGACTCCCGCAGCATGCGATAGAAGGCGGGACGCGCTTCCGGGTCTTCGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-8F
@SRR6576292.5 5/2
GCCGTGGAGCTCTGTACACCGGTGTCTCTGTCCTGGTGGCTCTGCTCTTGGCTGGGCAGGCCACCACTGCTTAGTTCCTGTACCAGCAACAGGGCCGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576292_1.fastq

Printing command:
fastqc --outdir SRR6576292_1.fastq

Analysis complete for SRR6576292_1.fastq

Processing SRR6576292_2.fastq

Printing command:
fastqc --outdir SRR6576292_2.fastq

Analysis complete for SRR6576292_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 83M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H16-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:46 SRR6576292_1.fastq
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:46 SRR6576292_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:20 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================