-----------------------
Start of variable list:
-----------------------
Sample_ID:
N9-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 19:49:50 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791392
Current job name : Step_02_N9-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/8791392.1.linga

Loading required modules...


List files in scratch directory:

total 35M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 88 root   root      180K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 N9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:49 SRR6576656_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:49 SRR6576656_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576656_1.fastq <==
@SRR6576656.1 1/1
GTTTTCTACTGTGTGCTTTTTGTTTTGTTTGAGACAGAGTCTTATCCCAGGCTTGTCTCAAGCTTATGTAGTTGAGGCTGGCCTTGAATTCTCAGTCCTC
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFF8FFFFFFFFFFFF8FFFFFFFFFFFF-FFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576656.2 2/1
GTGTCGGATGCCCGCTGTGTGTTTGACATGGCAACAGAAGTTGGTTTCAGCATGCATCTGCTTGATATTGGTGGTGGCTTTCCTGGATCTGAAGATACAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576656.3 3/1
TCACTGTGTTGGGCGCTGGGCCCCTAGTTTCTGGAGCTGGGAAGTTGGGCGACGGGCTCCGTCCCTGTCCTTCAGCTTCCAGCGTTCCTGGGTTTCCTTC
+
F8FFF-FF-FFFFFFFFFFFFFFFFF8FFF8FFFFF8FF8FFFFFF-FFFFF--FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576656.4 4/1
GCTCTAGGTCTTCCAGGTCTCCAGAGATCTGCAGCAGGAGGAACCCCAAGGGTTTGATGGTGAACCTCCCAGTTGGGAAGGTTAAACGGCCTTCATAGCT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576656.5 5/1
ACGCAGAGTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576656_2.fastq <==
@SRR6576656.1 1/2
CAACAAACCTTTCCTCCTCACGTGGCTTTAGCCAGGGGTTTTTATCATGGCAGCAAGAGAACTAACTAACCCAGCACAGCATACAAGAGGCCCTAGGTCC
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576656.2 2/2
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAATTATTTTTTATGCAAACGTTAAATAATATGCCAAATATTAAATGGCATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F------FF--F---F----F--FF-----------F-F--F---------
@SRR6576656.3 3/2
GTACATACTTCTTTCAGCATAGCATTTAATACCTCTTCATTGATAATGGTGGCATTGCTCAATGAGCGTAATGCTGATGTTATTTTTCTTCCAAGATCTG
+
F8F-FFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFF8-FFFF-F-F--FF8F
@SRR6576656.4 4/2
GGCGGGCGCTCTCCCTACCCTGGGGCCCGGCTGGCAGCGCCAAAATCCGGACCCGCCGGTCTCCCGCACCCGCTCGCTGCTGCTGGACGCCGCGTCGGGC
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFF
@SRR6576656.5 5/2
CAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGTCCGCCCGCCCGCTCCCAAGATCCAACTACG
+
FFFFFFF-F8FFFFFFFFF8F8FFFFF-FFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-F-F-FFFFF-FFF

Starting FASTQC command


Processing SRR6576656_1.fastq

Printing command:
fastqc --outdir SRR6576656_1.fastq

Analysis complete for SRR6576656_1.fastq

Processing SRR6576656_2.fastq

Printing command:
fastqc --outdir SRR6576656_2.fastq

Analysis complete for SRR6576656_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 186M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 88 root   root      180K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 N9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  93M Oct 12 19:49 SRR6576656_1.fastq
-rw-r--r--   1 kkarri waxmanlab  93M Oct 12 19:49 SRR6576656_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:15 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================