-----------------------
Start of variable list:
-----------------------
Sample_ID:
A4-MAA000907-3_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 19:41:26 EDT 2018
Running on node : scc-ka8
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790686
Current job name : Step_02_A4-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790686.1.linga

Loading required modules...


List files in scratch directory:

total 22M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 55 root   root       72K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 A4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6575504_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6575504_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575504_1.fastq <==
@SRR6575504.1 1/1
GGATAAGAAGGAGACTGTCTGGATGCTTCCTGAGTTTGGCCAATTGGCAAGCTTTGACCCCCAAGGTGGACTGCAAAACATAGCTGTAGTAAAACACAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575504.2 2/1
TCTTAAACACAGTGAACTATTCCTGACTCAGATCTGTGTTTACAGGTAAATTACTAAACGTGGTCTCCAACCACTTCCTCTTAATTTGCCATCAACTAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFF-F-FF-FFFFFFFFFFFF-FFFFFFFFFF
@SRR6575504.3 3/1
CGCCCAGGGCGGGCTGCTGGCCGCCCTGCGTACCGGCGTGCCCGTGCCGCAGCGCGTGGCGATCGCCGGCTTCAACGATCTCGGCGGCAGCGACCAGATG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFF
@SRR6575504.4 4/1
ATATTGGTGAGTAGGCCAAGGGTTAATAGTGTAATTGAATTATAGTGAAATCATATTACTAGACCTGATGTTAGAAGGAGGGCTGAAAAGGCTCCAGTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575504.5 5/1
ATACTTTTATTTAGATTGCAGCACTAACAACATGATAGACTTTCACAAATCATAAAGCACACACTATTTAAAATATTTTGCTGTTCACAATTTGAATGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFF

==> SRR6575504_2.fastq <==
@SRR6575504.1 1/2
CAAGTTGGGGGTCACTTGAAGAAGAGAAAGAACACCATGAATTGGTCCAGAAAACACACTGTGCCAGGTCACCCAGCACACCACTTCTTCCCTGAAGAGG
+
FFFFFFFFFFFFFFFF8FFFF8-FFFFFFFFFFFF-F-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFF-FFFFFFFF-FFFF-F8-
@SRR6575504.2 2/2
ATACTAACAAACCTGCAGTGGAAGCTCACTTGATACAGTGCTTGTACCACAAGCCTAAATCTCTGAGCTCCTTCCTCAGCACACAGTTATAATAATCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575504.3 3/2
TCCATGGAGACGACCATGCCGAGAACGAACCTGCGCAGGAACAGCGGCGAAGCAGCGGCGACTGCCGTCGGCGCCGCGCAAGAACAGACGCCGCCCCCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFF-FFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575504.4 4/2
CCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACA
+
FFFFFFFFFFFFF8F-FFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6575504.5 5/2
TGTCTGCTGCGAAAGCCATCGCAGACCACATCAGAGACATCTGGTTTGGAACCCCAGAGGGAGAGTTCGTGTCGATGGGTGTTATCTCTGATGGCAACTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FF-F8F-FFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575504_1.fastq

Printing command:
fastqc --outdir SRR6575504_1.fastq

Analysis complete for SRR6575504_1.fastq

Processing SRR6575504_2.fastq

Printing command:
fastqc --outdir SRR6575504_2.fastq

Analysis complete for SRR6575504_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 115M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 55 root   root       72K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 A4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:41 SRR6575504_1.fastq
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:41 SRR6575504_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:45 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================