-----------------------
Start of variable list:
-----------------------
Sample_ID:
H1-MAA100039-3_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 19:46:11 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791228
Current job name : Step_02_H1-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791228.1.linga

Loading required modules...


List files in scratch directory:

total 43M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:46 SRR6576965_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:46 SRR6576965_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576965_1.fastq <==
@SRR6576965.1 1/1
GGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576965.2 2/1
GTCAGGAGGCAAAGCTTCAGTCATAATACCATCAGGTGATGTTTCCTCCTGCAGCTGCTTAACCTCCCGATCACAGCTCTCCATCCTCAGCTTCTTCAAC
+
---FFF-FFFFFFFFF-FF8F88FFFFFFFFFFFF-FFFFFFFFFFFFFF-F-FFF-FFFFFF-FFFFFFFF-F--FFF-FFFFFF-FFF-F-FFFF-FF
@SRR6576965.3 3/1
GTACAGTGAAACTGCGAATGGCTCTTTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576965.4 4/1
GAGGAGAGCCGTGCGCAGCGGCGTGTGTGGGGCCGTGTGCAGACCCGCGTGTGGCGCAGGCAAGGACCCTGAAAATAAACAGCCGCTGCTTTGCGAGTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576965.5 5/1
GTTGTCCCCAAGAACTAGGCGAGAAGCACAGCTCCGGAACTCTGCCAGGCCCAGGATGGGCAGGTACTCGTGGTTGAGGCTGTTGTCGTTAGCAATCTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576965_2.fastq <==
@SRR6576965.1 1/2
GCATACTATTATCCTGGCCTCTGACAAGAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576965.2 2/2
GCCGTATATCTTCCCAGACTCTCCGGGGGGCACTTCCTTCGAGAGATATGAGTGCTACAAGGTTCCTGAATGGTGCTTAGATTACTGGCATCCCTCTGAG
+
FF--FFFFFFFFFFFFFFFFFFF8F-F-FFFFFF-F-FFFF-FFFFFFFFFFFF-FF-F---FFFF-F-FFF-F-FFFFFFFFFFFFFFFF8FFFF--F8
@SRR6576965.3 3/2
ATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCAGCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576965.4 4/2
CAATTGTGCATTCCCGTGCAAGATGCCCTGACTCGCCACAGCGGTAACAGTTGACTTCACTTGTCTTGCTGCAATTGATGGCTACATGACCAGTTTCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFF-FFF--FFFFFFFFFFF--F--FFFFF--FFFFFFFF-F-F-FF
@SRR6576965.5 5/2
ATTCTGTCGCGATGGCGCCTCCATCAGTCTTTGCCCAGGTTCCGCAAGCTCCTCCGGTTCTGGTCTTTAAGCTCACTGCGGACTTCCGGGATGATCCAGA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576965_1.fastq

Printing command:
fastqc --outdir SRR6576965_1.fastq

Analysis complete for SRR6576965_1.fastq

Processing SRR6576965_2.fastq

Printing command:
fastqc --outdir SRR6576965_2.fastq

Analysis complete for SRR6576965_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 256M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 80 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:46 SRR6576965_1.fastq
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:46 SRR6576965_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:43 EDT 2018
0 hours, 0 minutes and 32 seconds elapsed.
==========================================================