-----------------------
Start of variable list:
-----------------------
Sample_ID:
G5-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 19:46:08 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791202
Current job name : Step_02_G5-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/8791202.1.linga

Loading required modules...


List files in scratch directory:

total 31M
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 G5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:46 SRR6575261_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6575261_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575261_1.fastq <==
@SRR6575261.1 1/1
GCATACTATTATCCTGGCCTCTGACAAGAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTA
+
F8FFFFFFFFFFFFF-FFFFFFFFFFF88FFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575261.2 2/1
CATTAATACTTTGGGAAGGGCCTCTCCATGAACACCAACCCACTCCTTGCTCTCTTTGGATATTGCCCACCTGGAGGCTCAGGCCATTCTTCATTCTCGG
+
8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575261.3 3/1
GGGTAGTCTGAGAAGGTTGTGGTTGTGATGTGTTTAGGATAAGGCGTCTTTGCATCTAGTGACAAGGTTTGGACCCTCAGTCGAGAAGCAGGTGTCCTTG
+
FFF--FFFFFFFFFFF-FF8FFFFFFF8FFFFFFF-8FFFFF8FFFFFFFFFFF-FFFFFFFF-FF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575261.4 4/1
CAGCCAACTGATGAAGAGATGCTGTTCATCTACAGTCACTTCAAACAAGCTACTGTGGGCGATGTAAATACAGATCGGCCGGGGCTCTTGGACCTCAAGG
+
FFFFFFF-FFFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF--FFFF-FFFFFFFFF-FFFFFFFFFFFFF-FF
@SRR6575261.5 5/1
CTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGAGAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGTTTTGAGTTCAGAC
+
F8FFFFFFF-FFFFFF-FFFFFFFFFF8FFFFFFFFFF8F-FF-FFFFFFF-FF-FFFFF--FF-FFFFFFFF-FFFF-F---FFF--FF--FFFFFF-F

==> SRR6575261_2.fastq <==
@SRR6575261.1 1/2
GGGGAGGCTGTATGGATAGGAAGGGCTGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGA
+
F8FFF-FF-F8FFFFFFFFFFFFFF-FFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575261.2 2/2
ACCCTAGTGTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTG
+
F8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575261.3 3/2
ATCCTGAACCGTGTGTGTCTGCTGCATGAGAAGACCCCAGTGAGTGAGCATGTTACCAAGTGCTGTAGTGGATCCCTGGTGGAAAGGCGGCCATGCTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575261.4 4/2
GGTCACACGTGTGGCTGGCCACCAAATCTGGTGATTTATATTCCGTATTTCTTCTTTAGCTCGTCTACCTTTTCCACATAGGTCTTCATGGCACTTTCCT
+
FF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575261.5 5/2
TCTCTGTAAGACACGATGGAAAGCAGATCACAGAACTTCTTACTGGATGCTGTATGGATAGGAAGGACTGATCCTGGAGTCCTGGTGAGAAGTCTCCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF--FFF--FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFF8

Starting FASTQC command


Processing SRR6575261_1.fastq

Printing command:
fastqc --outdir SRR6575261_1.fastq

Analysis complete for SRR6575261_1.fastq

Processing SRR6575261_2.fastq

Printing command:
fastqc --outdir SRR6575261_2.fastq

Analysis complete for SRR6575261_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 161M
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 G5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  81M Oct 12 19:46 SRR6575261_1.fastq
-rw-r--r--   1 kkarri waxmanlab  81M Oct 12 19:46 SRR6575261_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:35 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================