-----------------------
Start of variable list:
-----------------------
Sample_ID:
C14-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-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790737
Current job name : Step_02_C14-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/8790737.1.linga

Loading required modules...


List files in scratch directory:

total 40M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 C14-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576201_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576201_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576201_1.fastq <==
@SRR6576201.1 1/1
CTCAGGACCTTTGGAAGAGCAGTCAGCGCTGAGCCATCTCTCCAGCCACCCACATTCAAATTATTATTCTCAGTGTGGAAGTGAGGAGCTGCAGCTCAGG
+
FFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-F-FF-FFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576201.2 2/1
GTGCTAGATCGATTTAGTCTAGTTCTAAATCAAATTCTTAAGGCTGGTATGAAGTCCATCCTCAATGCCAGTCAATGCCAAGGCAGGGTTCCCTAAGCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFF-FFF-FFFFFFFFF
@SRR6576201.3 3/1
ACTTAGATATGAAATTTCCCCTATCATCTTCATTTGCTATTCTATTATTGTTTCATCCCCGTCTCCATTGCCAGAGGCAAGCCATTCTGCCCTTGAAGGC
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576201.4 4/1
GGCATGACTCTCTCGGTTACAAGCACCCTCTGCTTGAGTTTGATTAGCCCGATATCCACCACGGAGTGGTTGGGGTGGAGAACGACCTTCTCAATCTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576201.5 5/1
GTAAAAAGGGATCACTCTGGAGTTCAGCGGACAGAACTCTTGCCTGGTGACCGGGAAAATCTGGCCATTCAGACCCGGGGTGGTCCAGAAAAGCATGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8FFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFF-FFFFF-FFFFFFFFFFFFFFFF-

==> SRR6576201_2.fastq <==
@SRR6576201.1 1/2
TGCCTGGACTGTACTGAGTGACAGACGATGTGTTCAGGTCTCTCCTGTGACATCCAGAGCCCTCAGTTCTCTTTACACACCATTGTCTGATGTTCCCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-F-FFFFFFFFFFFF-FFFFFFFFFFFFFF8FF-FF
@SRR6576201.2 2/2
GTATACAGAGGGAGGGACATACAATATTTAATAGGATATTTCTACAGAACAATAACTTATATTATGTCCTTGTAAAAATCTGTACCTCTTTAAAACATTT
+
FFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFF-F-FFFFFFFFFFFFFFFFF8FFFF
@SRR6576201.3 3/2
TTTACAATCTGTGTGAATTCTGCCAATGCGGCCAAGCTGCGCACCTCACTGTGTCCATGTGAATAAGGAAGAAAAGCAAATTCCTCTGGCTTCCCAGAGC
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8F8FFF
@SRR6576201.4 4/2
GTGGACCAGGTGCAGCGCATCATCGGTGGCTCTATGGATGCCAAAGGCAGCTTTCCTTGGCAGGCCAAGATGATCTCCCGCCACGGACTCACCACCGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576201.5 5/2
TGTGTTATCTTTGATTTCTCTGTGTAAAACCAGCTGGCTGTAATAAAGTGTTAGTGGGTTAGGTTAAGAGAAGTGTGTCAGGCAAGAGCAGGGTTATAGC
+
-F-FFFFFFF8FFFFFFFFFFFF8FF-FFF-F-FFFFFFF-FFFFFFFFFF-F-F-FFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFF-FFFFF8FF8-

Starting FASTQC command


Processing SRR6576201_1.fastq

Printing command:
fastqc --outdir SRR6576201_1.fastq

Analysis complete for SRR6576201_1.fastq

Processing SRR6576201_2.fastq

Printing command:
fastqc --outdir SRR6576201_2.fastq

Analysis complete for SRR6576201_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 204M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 C14-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 102M Oct 12 19:41 SRR6576201_1.fastq
-rw-r--r--    1 kkarri waxmanlab 102M Oct 12 19:41 SRR6576201_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:57 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================