-----------------------
Start of variable list:
-----------------------
Sample_ID:
E5-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 19:44:31 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791121
Current job name : Step_02_E5-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/8791121.1.linga

Loading required modules...


List files in scratch directory:

total 42M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:44 SRR6575207_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:44 SRR6575207_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575207_1.fastq <==
@SRR6575207.1 1/1
CTGTAAGAGATGAAGAGTGCTCGGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTAC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575207.2 2/1
TTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGG
+
FFFFFF--FFFFFFFFFFFFF8FFFF88FFFFFFF-FFFFF-FFFFF-FFFF-FFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFF-FFFF--FFFFFFFF
@SRR6575207.3 3/1
AGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575207.4 4/1
GTCCAAGACTTGACAGAGGCTCCAGGGCGGTTACAAAGCTGCCTAGTGGCTTGAGAGGTTCATTCAGGTGGAGGTCCCAGGGCGGGCTGGTGCAGAGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575207.5 5/1
CTCCTGGGGACCATCCCAGGTGCTGGAGGCACTCAGAGACTCACCCGAGCAGTCGGCAAATCGCTAGCAATGGAGATGGACCTCACTGGTGACCGCATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8FFFFFFF8FFFFFFFFFFFF--F--FFFF-FFFFFFFFFFF-FFFFFF-FF-FFFFFFFFFF-FFF-FF

==> SRR6575207_2.fastq <==
@SRR6575207.1 1/2
NCATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCATCCTTTTCGTTAATG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575207.2 2/2
GTACCTGGATGATCCTGCCAGTAGCATATGCGTGTCTCATAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCA
+
-FFFFFFF-8FFFFFF8FF8FF-FFFF-FFF-FFFFFF--FFFFFFF---FFFFFF-FFFFFF-FFFF-FFFFF-FFFFFF--F8FFFFFF-FFFFF-F8
@SRR6575207.3 3/2
GATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-F-FF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575207.4 4/2
CTTGGATCTGCATGCCCTGGGTTCTGCCCGCGCGGACCCTCATCTCTGTGACTTCCTGGAAAGCCACTATCTGGATAAGGAGGTGAAACTCATCAAGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575207.5 5/2
CGGTAAAGCTGCCAGTTCTCAGTGGTCTATGTCGTTGGCCTTCCTTTTCTCTACAAATGCAGTCATCCCATCTCTCCGCTCATCGGTGGCAAAGGTGGAA
+
8F-FF-FFF8FFFFFFF-FFFFF8FFF---F---FFF-FFFFFF---FF-FFFF---FFF-F-FF-F-F-FFFF-FFF-FFF-FF--FF--FFFFFFF8-

Starting FASTQC command


Processing SRR6575207_1.fastq

Printing command:
fastqc --outdir SRR6575207_1.fastq

Analysis complete for SRR6575207_1.fastq

Processing SRR6575207_2.fastq

Printing command:
fastqc --outdir SRR6575207_2.fastq

Analysis complete for SRR6575207_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 241M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 121M Oct 12 19:44 SRR6575207_1.fastq
-rw-r--r--   1 kkarri waxmanlab 121M Oct 12 19:44 SRR6575207_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:02 EDT 2018
0 hours, 0 minutes and 31 seconds elapsed.
==========================================================