-----------------------
Start of variable list:
-----------------------
Sample_ID:
E4-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 19:41:27 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790769
Current job name : Step_02_E4-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/8790769.1.linga

Loading required modules...


List files in scratch directory:

total 20M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 45 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.7M Oct 12 19:41 SRR6576271_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576271_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576271_1.fastq <==
@SRR6576271.1 1/1
CATGGGGGAAGTGCGGACATTGCCCAGGGCGTCTTGGTGGTGGTGAGTGAGGTTTAGGGAGCTGGGGCTCGCGCAGCGGGTGTCTGCCAGCGGAGCTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576271.2 2/1
CTCTGGATGCGTTTCGAGATGCCCTCATGCTCAGCCAGCTGACCACAGAGCACTGCATACCACAGGTGGCACGCAGCACTCTCATCTCCTTTCTTCAGAG
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFF-FFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576271.3 3/1
CATGAGGTTCTACTTTACCAACTGGCACGGAACCAATGACAACGAACAGTCTGTATGGCGACATTCTCCAAAGAAGCAGAAAAACGGCTATGAGAAGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576271.4 4/1
AGATTGCAGGATAGTTATGAACAGTCAGGAAAATAATTGATTACCATTGGAACAGGTTTTTTTTATAACTAATATTTGATCTTGCTTTCAAGTGGTCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576271.5 5/1
ACCTTCTCTAATCTTTTAATGTGTCTGTTTGCAATATGGGGGTTAGACTTTTTATCATTACCTTTTCTTTTCCTTGGCTGTACATTTACCTTTTTCACAA
+
FFFFFFF-FFFFF-FFFFFF8FFFFF8FFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFF-FF-FFFFFFFFFFF

==> SRR6576271_2.fastq <==
@SRR6576271.1 1/2
GAGCAGGACTGGAATGACAATGCAAGGAATGCACACCATTGTCCCAGGTTGGAGCTCCGACACGTGCCGGTCCAAAGGGAGGAAAGCCGCGAGAGAAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576271.2 2/2
GGATTCCTGTGCGTCCTTTACAGCCAGCGATGGAAACGGACCCAGCGCCATGGCCGGAGTCACAGTCTGCCCAACTCCCTGGACTATGCGCAGGCTTCAG
+
F8FFF-FFFFFF8F8FFFFFFFF8-F-FFFFFFFFFFFF-F-FF-FFF-FF-FFFFFF-FFF-FFFFFFFFFF-FFFFFFFFF-FFF-F-F8F--8F-FF
@SRR6576271.3 3/2
TTCGAATGGCATCGACTCAATTCATTTTCTGATGAAATCAGTAGCATAGAAGTCTCAAATATTTCAGCTCCATAATGATTTGTCAAAGTTTCCAAGGTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFF-FFFF
@SRR6576271.4 4/2
TCTCTGTATAGCCCTACCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAA
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFF
@SRR6576271.5 5/2
ATTTAGGCCTTTTTATTTTAATAAATAACTTCAGGTAATAGCACTGTCAAAATGAAAAGGCACTTAAAACAAGATTGTGACTAGTTCGAGACAGAGCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-F-FFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576271_1.fastq

Printing command:
fastqc --outdir SRR6576271_1.fastq

Analysis complete for SRR6576271_1.fastq

Processing SRR6576271_2.fastq

Printing command:
fastqc --outdir SRR6576271_2.fastq

Analysis complete for SRR6576271_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 101M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 45 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:41 SRR6576271_1.fastq
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:41 SRR6576271_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:40 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================