-----------------------
Start of variable list:
-----------------------
Sample_ID:
F2-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 19:44:29 EDT 2018
Running on node : scc-yd1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791154
Current job name : Step_02_F2-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/8791154.1.y

Loading required modules...


List files in scratch directory:

total 96M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:44 SRR6576071_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:44 SRR6576071_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576071_1.fastq <==
@SRR6576071.1 1/1
GNGCCATCTCACCAGCCCGCTTGGCATTTTTTTAAACAGTCATTTTGTAAGGGATAATGATGGGCAGCAGGTCTCATGAACGAGGAATGACACAGAGTTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576071.2 2/1
GCTGTAGTGGATCCCTGGTGGAAAGGCGACCATGCTTCTCTGCTCTGACAGTTGATGAAACATATGTCCCCAAAGAGTTTAAAGCTGAGACCTTCACCTT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576071.3 3/1
TAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTG
+
FFF8FFFFFFF-FFFF-FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFF-FFFFFF--F-FFFFFF-FFFFF
@SRR6576071.4 4/1
ATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTGTGATTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF8FFFFFFFF-FFF-FFFFF-FFFFFFFF-FFFFFF-FFFF-FF-FFFFFFFFFFF-FF-FFFF-FFFFF
@SRR6576071.5 5/1
GCCTATACCGGGAGCTGGTCCATCAGTCCAACACTTCCAACATCTTCTTCTCCCCAGTGAGCATTGCCACAGCCTTTGCTATGCTCTCCCTAGGGAGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576071_2.fastq <==
@SRR6576071.1 1/2
NAACTNTTTCTGCTTTTGTCTGCTATTCTGCAGCATTTTAATCTGAAGTCTCTGGTTGACCCTAAGGATATCGACCTCAGCCCTGTTACAATTGGCTTTG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576071.2 2/2
GGTTTGGACCCTCAGTCGAGAAGCAGGTGTCCTTGTCAGCAGCCTTGCAACATGTATCCAGGAACTGTGCAAAGTCATCCATGACAGTCTTCAGTTGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576071.3 3/2
GGGACACTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576071.4 4/2
ATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGACTTTAAGAACTAAGGATTTCTCCAAG
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFF-FFFFF
@SRR6576071.5 5/2
CCTCAGCTATCTTTCCTTGGGTTCCCTTCTCCACAAAATCATTAATCACTTTCTTGGCCTCCTCTGACTCTGCAAAGTTGACAGAGAAGACTTCTGCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF

Starting FASTQC command


Processing SRR6576071_1.fastq

Printing command:
fastqc --outdir SRR6576071_1.fastq

Analysis complete for SRR6576071_1.fastq

Processing SRR6576071_2.fastq

Printing command:
fastqc --outdir SRR6576071_2.fastq

Analysis complete for SRR6576071_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 546M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 273M Oct 12 19:44 SRR6576071_1.fastq
-rw-r--r--   1 kkarri waxmanlab 273M Oct 12 19:44 SRR6576071_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:54 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================