-----------------------
Start of variable list:
-----------------------
Sample_ID:
J8-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 19:49:49 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791341
Current job name : Step_02_J8-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/8791341.1.linga

Loading required modules...


List files in scratch directory:

total 28M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 102 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 J8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  14M Oct 12 19:49 SRR6576474_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  14M Oct 12 19:49 SRR6576474_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576474_1.fastq <==
@SRR6576474.1 1/1
GTAATGAGGCGAGCGCCGCCAATATGCACTGTACATTCCACGAGCATTGCCTTCTTATTTTACTTCTTTTAGCTGTTTAACTTTGTAAGATGCAAAGAGG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFF-FFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576474.2 2/1
CCCCACCGACAGCAGCGGTGTCCACGCCACCTGTGCCTCGCTTCTGAAGCCGCAGCCGCTTGAGCACCTCCGAGAACATCTCCACCTTCCCCAGGTGGGG
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFFFFF-F-FFFFFF-FFFFFFFFFFFFFFFF-FFFF---F-FFFFFFFF-FFFF
@SRR6576474.3 3/1
GAGCTGCAGAGCTCCCAAGTCACACAAGAACTGACGGCACTGATGGAGGACACTATGACGGAAGTAAAGGCTTACAAAAAGGAGCTGGAGGAACAGCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576474.4 4/1
GGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGC
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576474.5 5/1
ATTCTGCTCCCCCTGAATCTTGGCAGTGAGGGCTTTGGTCGCCTGCAGATCTGCCTTCAAACTCTGCATCTCTGTCTTGGCCCTCTGAAGATTGCTCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF

==> SRR6576474_2.fastq <==
@SRR6576474.1 1/2
GCATTTTACATCCTGCAGGACATCTTTGACCATCTTGAATTTTCCTCTCTATTTCATCATCTCCCACCCAGCTTTTTCCTTCACCAACATGCAAGTTCTT
+
FFF-FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-8FFFFFFFF
@SRR6576474.2 2/2
CTCAAGAGCATGACTGAGGCGGAGCAGCAGCAGCTCATTGACGACCACTTCCTCTACGAAAAGCCTGTGTCGCCTCTGCTGCTGGCCTCCAACATGGCCC
+
FFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFF--FF-F--FFF-FFFFFFFFFFFFFFFFF-FFFFF-F-F-F-FFFFF---F-
@SRR6576474.3 3/2
CTCCGAGTCGGGCCTGTGCCGCCTGCACCTCTTTGCCCAGCCTGGCCCGTGTCTCCTCCGCCACTGGACCCAGCTGTTCCTCCAGCTCCTTTTTGTAAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8--FF8FFF
@SRR6576474.4 4/2
GGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCTTTAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFF-FFFFFFFFFFFF-FFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFF--FF8FFFFF
@SRR6576474.5 5/2
ATGGTATGGAAAGGGCTGGTGAAAAGATGAACTCGTTAAAGAAAGAGCTGGAAACACTCACTGCTCAGACTCAAAAGGCAAATGGCCACCTGGAGCAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FF-FFFFF-8-FFFFFFFF-FFFF8

Starting FASTQC command


Processing SRR6576474_1.fastq

Printing command:
fastqc --outdir SRR6576474_1.fastq

Analysis complete for SRR6576474_1.fastq

Processing SRR6576474_2.fastq

Printing command:
fastqc --outdir SRR6576474_2.fastq

Analysis complete for SRR6576474_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 142M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 J8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  71M Oct 12 19:49 SRR6576474_1.fastq
-rw-r--r--    1 kkarri waxmanlab  71M Oct 12 19:49 SRR6576474_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:10 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================