-----------------------
Start of variable list:
-----------------------
Sample_ID:
G13-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 19:46:08 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791190
Current job name : Step_02_G13-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/8791190.1.linga

Loading required modules...


List files in scratch directory:

total 28M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6576203_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6576203_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576203_1.fastq <==
@SRR6576203.1 1/1
ATCCAGACGGCCGTGCGCCTGCTGCTGCCCGGGGAGCTGGCCAAGCACGCGGTGTCGGAGGGCACCAAGGCCGTCACCAAGTACACCAGCTCCAAGTGAT
+
FF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576203.2 2/1
ACCCTAGCCAGCCCGCTTCGATGACTCAGGGCACCCAAGGAACAATCCTCCCAGCCTCCAACTTTGATGCTATGAGAGATGCAGAAATTCTCCGCAAAGC
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576203.3 3/1
GAGCAAATCTGTGAATGGCGACTATGCGCCTAGTCAACCAGATGTGTGCTAGCCCGTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGAAAGCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576203.4 4/1
CCAATGAAGCGGTTCTCCACGATGTCAATGCGACCCACTCCGTGCTTGCCCGCAACTTCGTTCAGGTACATGAAGAGTTCCAGGGATGTGGTGCGGGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576203.5 5/1
CATTGATAAAAAAAAAAAAAAAAAAAAAAAAGTACCTGTCTCTTATAAACAACACCGAGCCCACGAGACAATCACTGATATCGTTTGCCGTCATCTGCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF888888FFF-F8--F----F-F-FFF-F-F-F-FF-FF---F-----F---FF-------F--F

==> SRR6576203_2.fastq <==
@SRR6576203.1 1/2
AAATGGTGCTTCTCAGTTGTTCCTTGAGTTCTGAAACTATGGTGGTTAATCTGCTAGTATCACCCATTTGCACTGTCTTGAGGTTACAGCATCCAGCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8
@SRR6576203.2 2/2
ACATGGACACGAGGAGACGTTCAAAATGTCCCGAGGTATCTGACCTAATGTCCTTCTCAAGGTCTCGTCCAAATTCTAATTGGTAACATCTAACAATGTC
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FFFFFFFFFFF8
@SRR6576203.3 3/2
CCCTTTTGAGCAATGATTGCACAACCTGCGATCACCTTATACAGAATTATCAATCAAGCTCCCCGAGGAGCGGACTTGTAAGGACCGCCGCTGTCGCTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFF
@SRR6576203.4 4/2
GTTTTACAACCGGTTCAAGGGCCGAAATGATCTGATGGAGTATGCAAAGCAACACGGAATCCCCATCCCTGTCACCCCCAAGAGCCCCTGGAGTATGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6576203.5 5/2
GTACTTTTTTTTTTTTTTTTTTTTTTTTATAAATGCTGTATCTTAAACACAAATGACGCTGCCGACCAGAAGGAAGGGGGTGTTATAGGGGGTGGCCGGG
+
FFFFFFFFFFF8FFFFFFFFFFFFF8FFF88FF8-F-F-----FF-F-F-F----F----FFF-F-----F-FFF---------------------8---

Starting FASTQC command


Processing SRR6576203_1.fastq

Printing command:
fastqc --outdir SRR6576203_1.fastq

Analysis complete for SRR6576203_1.fastq

Processing SRR6576203_2.fastq

Printing command:
fastqc --outdir SRR6576203_2.fastq

Analysis complete for SRR6576203_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 148M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  74M Oct 12 19:46 SRR6576203_1.fastq
-rw-r--r--   1 kkarri waxmanlab  74M Oct 12 19:46 SRR6576203_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:33 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================