-----------------------
Start of variable list:
-----------------------
Sample_ID:
O7-MAA000377-3_9_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 19:42:18 EDT 2018
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790889
Current job name : Step_02_O7-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790889.1.linga

Loading required modules...


List files in scratch directory:

total 5.1M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 102 root   root      128K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 O7-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 2.6M Oct 12 19:42 SRR6576913_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab 2.4M Oct 12 19:42 SRR6576913_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576913_1.fastq <==
@SRR6576913.1 1/1
TACTTATTAAAGCCAAGAAAAATAAAAACAAGAATGTAAAGCCTGCCGTTTTAAACTGATAGTATTTCTCTTCTGCTTTATACACTAAACTCTGCTTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576913.2 2/1
TATCAACGCAGAGTACATGGGAAACTTCTGAGAAACCGAAACTGCCGCAGAAAGGGCAGACCCGCAGCGCGCTCCATCCTTTGCCCTTCAGTGCTGCCTT
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576913.3 3/1
GGCCAAGGTGCAGAGAGCTGTGTGCATGCTGAGCAACACCACAGCCATTGCTGAGACCTGGGCTCGCCTAGATCACAAGTTTGATCTGATGTATGCCAAG
+
FFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576913.4 4/1
CTTTTATTCTCGTTATCTGCACTCTGGGCACTTGTGAGTCAGTGTTAATCACCATCTAGATGCATCTTCTAAGCATCTCTGAAGAGGACCAAGAGCTTTC
+
-F8FFF-FF-FFFFFFF8FFFFFFF8FFF8FFF88FFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576913.5 5/1
ACTCTATATAGACCAGGATGGCCTTGAACACATAGAAATCCACCAGCCTCTGCCTTCCAAGTGCTATAAATAAATGTGTGCACCGCCTCCTCCAGTACTG
+
8-F--FFFFF-F8FFFF8FFF8FFFFFFF8FF8FFFFFFF8FFFF8FFFFFFFFFFFF-FFFFFFFFFF-F-FFF-FFFFFFFFFFFFFFFFFFFFF--F

==> SRR6576913_2.fastq <==
@SRR6576913.1 1/2
GAGACAGGGTTTCTTTGTATAGTCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576913.2 2/2
GGTGATAACAACCATCAGGATGCTGAGGACCAAGGTGCTGATGTTCAGGCACTTAGCAGTGGAGGCGTAGGCCTGGGCTCCAGTCACATCACCCACCATC
+
F-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-FFFFFFFFFFF
@SRR6576913.3 3/2
GCTCAAGGAATGGACTTAGTTCTCCTCTCCTTCTTCCTCCCCCTCGCCTTCCACAGAATCCACACCAACCTCCTCATAATCCTTCTCTAGGGCAGCCATG
+
8-FFFFFFFFFFFF8F8FFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576913.4 4/2
ACCCAGTTATGGACCATGTCAGTGGAGGAAGGACTAGGCTGGCAAGATGTACCCATTGAGACCACAATGGCATGAATCTAGTGGAGACAACCAACTGCTG
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFF-
@SRR6576913.5 5/2
TTTCCCCTCCTCCCTGCCCCATAGGGAGAAGAATCAAATGAGTCTGTAGATGCCAGCAGCAACTGGGAAATGCAAGAAAGTAATGTGATGAAATTGCAAT
+
FF-FFFFFFF8FFF8FF8FFFF8FF88FF8-8FFFFFFF-FFF-----F------FFFFF-FFFFFF--FFF-FFFF---F-FFF-FF-FFFF--FF---

Starting FASTQC command


Processing SRR6576913_1.fastq

Printing command:
fastqc --outdir SRR6576913_1.fastq

Analysis complete for SRR6576913_1.fastq

Processing SRR6576913_2.fastq

Printing command:
fastqc --outdir SRR6576913_2.fastq

Analysis complete for SRR6576913_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 24M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 101 root   root      128K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 O7-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  12M Oct 12 19:42 SRR6576913_1.fastq
-rw-r--r--    1 kkarri waxmanlab  12M Oct 12 19:42 SRR6576913_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:33 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================