-----------------------
Start of variable list:
-----------------------
Sample_ID:
A6-MAA100040-3_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 19:42:18 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790938
Current job name : Step_02_A6-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790938.1.linga

Loading required modules...


List files in scratch directory:

total 37M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:42 SRR6577003_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:42 SRR6577003_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577003_1.fastq <==
@SRR6577003.1 1/1
CTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCGTGACTTGGAGAATTCCTTAGTTCTTAAATTCCAAACTGT
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFFFFFFFFF-FF--FFFFFFFFFF-FFFFFF-FFF--FFF-FF-FF
@SRR6577003.2 2/1
ATCTTGGAGCGCACCTCCTCCATGTGCTCACGCACCTCCTCTAGGCGGTCACGGGCCTGGTTGCCCACTTCCTCCAGCCGCCCTCGGATGCGGTCACCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFF-F-FFFFFFFFFFFFFFFFF-FFFF
@SRR6577003.3 3/1
AAGGAACCCAATTCAGAAGGAAGGATGACTTCTTAGGGTGGTCATTTATGTGTGGGATCTACCACTTTTCCCACAAAGAGGGGGCTCTGAGAGTGTTCTT
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-
@SRR6577003.4 4/1
CTAACGCTCTACGTGGGGAAAAACCAGCTGGTGGAGATTGAGAAGGTCGTTCTCCACCCCAACCACTCCGTGGTGGATATCGGGCTAATCAAACTCAAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF
@SRR6577003.5 5/1
TTAGTGTACTGTGAAATCGACGGATCTGGAAATGGTTGGACCGTATTGCAGAAGAGGATTGATGGCAGTTTGGATTTCAAGAAGAACTGGATTCAGTATA
+
8FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FF-FF-FF-FFFFFFFFFFFFF

==> SRR6577003_2.fastq <==
@SRR6577003.1 1/2
CTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFF-FFFFFF-FFFFFFFF-FFFF-FFFFFFFFFFFFF8FFFFFFF-FF-F-88
@SRR6577003.2 2/2
GAACCGCTTCTGGGATTACCTGCGCTGGGTGCAGACGCTGTCTGACCAGGTCCAGGAAGAGCTGCAGAGCTCCCAAGTCACACAAGAACTGACGGCACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-F
@SRR6577003.3 3/2
TCTCTAAGTTCCTGCTAAACAGGCGCAGAAGGTTAGCCCAGATCCATATCCCCAGACTGTCCATCTCTGGAAACTATAACTTGGAGACACTCATGAGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFF--FF-FFFFFFFFFFFFFFFFFFF
@SRR6577003.4 4/2
CCTGAACCCAGTCCTTCAGGTCGGTCGCCCTCACGTACACACCATTCTCAGCGACAGCGCAGCTCTTGTCAAAGCTCAGGATCCCAGCTGCGTACCAGGT
+
FFFFFF-FFFF-8FFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFF8FFFFFFFFFFFF-FF
@SRR6577003.5 5/2
CCAGCGGCTTTTCCAGGTCGCCCAAATAATGCCGTCGTCGAAACCATTAGTAGTAGATGATTTTGAGTAAGTACCACCTTGGTGATAAACTCCATTGAGG
+
FFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFF---FFFF--FFF--F--FFFFFFFFFFFFFFF-FFF-FFFFF-F--FFFFFF---F-FFFFFF-FFFF

Starting FASTQC command


Processing SRR6577003_1.fastq

Printing command:
fastqc --outdir SRR6577003_1.fastq

Analysis complete for SRR6577003_1.fastq

Processing SRR6577003_2.fastq

Printing command:
fastqc --outdir SRR6577003_2.fastq

Analysis complete for SRR6577003_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 202M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 101M Oct 12 19:42 SRR6577003_1.fastq
-rw-r--r--   1 kkarri waxmanlab 101M Oct 12 19:42 SRR6577003_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:45 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================