-----------------------
Start of variable list:
-----------------------
Sample_ID:
B9-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 19:49:49 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791361
Current job name : Step_02_B9-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/8791361.1.linga

Loading required modules...


List files in scratch directory:

total 43M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 B9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:49 SRR6576103_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:49 SRR6576103_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576103_1.fastq <==
@SRR6576103.1 1/1
GTACATGGGGAGCGCGCAGCCGCAGCGCCGCCAGCATGCGCGCCGAGGCCCGCGGCGGCCTGGAGCGCTTCTGCAGTGCGGGCAAGGGCCGGGGGCTCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576103.2 2/1
GTTGAGTACAGCTTTCCATGTTTAGCTAAAAAGATACGGGTTCTCTCTCTCAAGATTATTTCCTCCTGGATAATGAAGCTGGTCCCCACTTCCTAGTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576103.3 3/1
GCCCTAATGTTATCCCCAGCTATGGGACTCCTAGATGTGACTGAGAACAAAGGTATTGCCAAAGAAGTTCTTACTCAGAGATTGGGACCCTGAAAAAGAC
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576103.4 4/1
GCTCACTGCTGTTACCCAGGTCTATAATTATATTTTATTGTTACTTCGGATTTCATCTAATTCACTCTCAGATGGATGCCAATACCACAGGATTAGTAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-F-FF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576103.5 5/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576103_2.fastq <==
@SRR6576103.1 1/2
NAATAGTGAAGCCATTACAGTTCACCTGGGCGAAGAGCACCACGAGACTGCTGTGGTCAGGGAATTCCAGGTACTTGGAGTAGAACTGGTGGAGAGCGGC
+
#FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFF-FFFF-FFFFF-FFF--FFFFFFFFFFF-FFFFFFFFFFF-FFFF
@SRR6576103.2 2/2
NCTTCCAACTTCTCAGTGCTTCAGACTGACCCTTCACCACCACATTTAAACAGCTGCTAACAAAACCAGCTTTTCTGTGACAGCAACAAGCCTAGCTAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576103.3 3/2
CAGTTGGATAATGCTTTTAAGAGCGTTAGTCAGCCATCGGTCATGGGGGCTGAACCACACTTTCTAGGACATGTGCCAAGTTTTGTCTCAGAGTCAATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576103.4 4/2
GGAAGGACTACTGTTGTTTTCAAGTTAGTATGGCAACTGTATAACTGTGTAACTGTGAATAGTTAAGAGCTGTGGTTGTCCCTGCAGTTAAAATTCTACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576103.5 5/2
GGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGGCTTAATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576103_1.fastq

Printing command:
fastqc --outdir SRR6576103_1.fastq

Analysis complete for SRR6576103_1.fastq

Processing SRR6576103_2.fastq

Printing command:
fastqc --outdir SRR6576103_2.fastq

Analysis complete for SRR6576103_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 230M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 B9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 115M Oct 12 19:49 SRR6576103_1.fastq
-rw-r--r--   1 kkarri waxmanlab 115M Oct 12 19:49 SRR6576103_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:07 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================