-----------------------
Start of variable list:
-----------------------
Sample_ID:
E12-MAA100140-3_57_F-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 19:44:31 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791103
Current job name : Step_02_E12-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791103.1.linga

Loading required modules...


List files in scratch directory:

total 60M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 E12-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  29M Oct 12 19:44 SRR6576066_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  31M Oct 12 19:44 SRR6576066_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576066_1.fastq <==
@SRR6576066.1 1/1
GTGTCTGAGAGCAAGGCTCTGTGCCACCCTTCATCTGTGGACTCACTCTCGACCAGTGCTGCTACAGAAGACCACGTCTCCATGGGAGGATGGGCAGCCA
+
FFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576066.2 2/1
GGTGCTATGATCGCGGCCTCGCCTGGTACCGGGGCCTAATGCCACGGACCCTGGATGGGCAGATCACCATGGAGAAGACGCCCAGCTACTTTGTGACTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576066.3 3/1
TGCCTTATGTGATAGATGCCTCTTTAAAACATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAAGCTATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576066.4 4/1
GAGCACGAGAATACCAAGTGCATCAGCTTCCGTGACCACATGAAGACCGTCCTTCCGCCTGATGGCCCCCGGCTTGCCTGTGTGAAGAAAACCTCCTATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576066.5 5/1
GAAGAGCGGCAGATCCTTGGTGAACTTGATTATCTGTTGAACCATAAACGTGTACATATCTGCAAAGTGAGTGAGCAGAGCCAACACGGGGCCCCGAGGC
+
-F-FFFFFFFFFFFFF-FF888FF8F88FF88FFFFFFF8FFFFF-FFFFF-F--F-FFFFF-FFF-FFF-F-F-FFFFF-FFFFF--F-FFFFF-F-FF

==> SRR6576066_2.fastq <==
@SRR6576066.1 1/2
GCTCAGGCCCATCTGATGTGCCTGTCCTCGAGGAAGCCCGTTAAAGATCGTCAGACTCTGGGATTGTGGCTGAGTTCTTTCGGAGAGATTCTAGTGAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F
@SRR6576066.2 2/2
NGGTCTTGGAGAGTGTCTGTGCATAATCAGAGATGGCCCGGGTCACGGGGTTCCGCACCACCACAATCAGCTTGGTATCTGGGGACATGCCATGGATTCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576066.3 3/2
CCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCACCATCATGCTATTAATGATATTAAAATCCCAACTATACCAAAGAATATCCCAATTATCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576066.4 4/2
CTTTACCACAGCCACAGCGTAGTAGTAGGTCTGTGGATGTTCCACTGATCCATAAAACTCCGCCGCCACGGGCTTCAGGTTGTTCGGAGTCAGGCCGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576066.5 5/2
CATGTGGCCTGCTTCCTCAGCGAAACAGGAGACCATGACAGCTATTCTAACAAAAGTAACCAAGTCCAGTGAAGAATCAAATGGTCCGAGAAACTGTTTC
+
F8--FFFFF8F-F8FF8-FF8FFFFF-FFFFF-FFF--F-FFF-F-FF-F------FFFFFF---FF-F--FF-FF--F--F-F-FF-FF-FF-F-----

Starting FASTQC command


Processing SRR6576066_1.fastq

Printing command:
fastqc --outdir SRR6576066_1.fastq

Analysis complete for SRR6576066_1.fastq

Processing SRR6576066_2.fastq

Printing command:
fastqc --outdir SRR6576066_2.fastq

Analysis complete for SRR6576066_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 352M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 E12-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 176M Oct 12 19:44 SRR6576066_1.fastq
-rw-r--r--    1 kkarri waxmanlab 176M Oct 12 19:44 SRR6576066_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:09 EDT 2018
0 hours, 0 minutes and 38 seconds elapsed.
==========================================================