-----------------------
Start of variable list:
-----------------------
Sample_ID:
F13-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 19:44:30 EDT 2018
Running on node : scc-wb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791143
Current job name : Step_02_F13-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/8791143.1.w-long

Loading required modules...


List files in scratch directory:

total 27M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 29 root   root       68K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:44 SRR6575814_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:44 SRR6575814_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575814_1.fastq <==
@SRR6575814.1 1/1
GTACATGGGGAGCGCGGGTCCTGTTGGTGAAAAGTCCCAGAAGTGCACAGGCTCGGCAGGACAACTTGCAGCCCTTCTCCCTGGATTCAGTCATTTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF8FFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFF--F-FFF-FFFF-FFFFFFF-FFFFF
@SRR6575814.2 2/1
GATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCT
+
FF-FFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFF8FFF--FFFFFFFFFFFF--FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575814.3 3/1
ATAGTACTGTAGATAGGACCCAGGGCTTGGATTTGCTTAACCAGCGCAGCCATCCAGCTGTGTGCCCAGCTCCTTGTTGCTTTTAGTAACCCCGATCCCC
+
FFFFFFF8FFFFFFFFFFFFFFFFFFF8FFFFF8FFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFF-FF--FFFF-FFF-FFFFFFFFFFFFF
@SRR6575814.4 4/1
ACCCCAAAGTCATTGTAGAGGTACTGTTCAAATACCCCATCACTCAGTGCCTTGCTGCCCCAGGCGTGTATCGAATGGTTCTTCAGCAGAAAACCTCCAA
+
-FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575814.5 5/1
GCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCATCTCGTCAGCGCTGGTCGTCTACCAGCTCGATAATTGGCGCAAGTTGTAGGTCGGGGGCACC
+
-8-FF8FFFFF8FFFFFFFFF8F8FFFFFFFF88F88F8FFF8FFF-8--FFFFFFFFFFF-FFFFFFFF-F-FFFFFFFFFFFF-FFFFFFFFFF-FF-

==> SRR6575814_2.fastq <==
@SRR6575814.1 1/2
CTCCCTTGCCAAAGCCAGCGCAGTCTTCTGGGTTGGCAAAAACCTTGTTGGTTATCCTCTGGAATGCGGTCGCAGAGCTCATGAACATCATCTTGGTAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-F-FFFFFFFFFFFFFFFF-FFF8FF8
@SRR6575814.2 2/2
AGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGA
+
F-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFF-F-FFFFFFFFFFFF-F-FFFFFFF-FFFF--FFFF-F-FFFFFFF-FFFFFFFFFFFF--FFFF-F-
@SRR6575814.3 3/2
CTCCAAACTAGTCTATAGAATCTGAGGGCAGGGCCATCCCCACCAGTCTCCAATACATTCAGTGCAGGGGTTCCTGCCCTCCCCACTAGTATCTAACCGC
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575814.4 4/2
GTCCATAGACCTCGTGGATGGAAAGACCTGTCCTTTGCTTCCACTGCTCATACTCCTCAGGCAGCAGGCTCTCCCCACCAGTAGTGCAATGCTCAAGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6575814.5 5/2
GGCGCTAGTAGATCACAGAACAACCGCCGCATACGGCCGATTGTCGCAGCCCGGGTCGATTATCACAACGGTGCAATCTCAGCTAAACCGACGCAGTTTT
+
FFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF-FFF-FFFFFF---FF-FFFFFFFFFFFF8-FF8FFF---F

Starting FASTQC command


Processing SRR6575814_1.fastq

Printing command:
fastqc --outdir SRR6575814_1.fastq

Analysis complete for SRR6575814_1.fastq

Processing SRR6575814_2.fastq

Printing command:
fastqc --outdir SRR6575814_2.fastq

Analysis complete for SRR6575814_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 138M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 29 root   root       68K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  69M Oct 12 19:44 SRR6575814_1.fastq
-rw-r--r--   1 kkarri waxmanlab  69M Oct 12 19:44 SRR6575814_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:43 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================