-----------------------
Start of variable list:
-----------------------
Sample_ID:
F6-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 19:46:09 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791171
Current job name : Step_02_F6-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/8791171.1.linga

Loading required modules...


List files in scratch directory:

total 141M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  68M Oct 12 19:46 SRR6576079_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  73M Oct 12 19:46 SRR6576079_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576079_1.fastq <==
@SRR6576079.1 1/1
TNGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAAT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576079.2 2/1
GCTGAGAGCCTCCTGGATCAGAGAGAGTGATGGTGGAGGCACAGAATAGGACTCTGGTGTGGCTTTGAAGTCTGAGGGTCTCTGGTAATTCTAACTCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576079.3 3/1
TTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576079.4 4/1
GCCAATCATAGGGATTCCATGATAGATCGCCTCGTAGACACCATTGGCCCCACCATGAGTTACAAAGGCTTTGGTTTTTGGATGACCAAGGAGGTCATTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--FFFFFFFF-FFFFFF-FFF-FFFF--F-FF
@SRR6576079.5 5/1
GTGCAAGGATCACACCTTTTGATTTGTGCCCATAGCCTATGTGATTATAGATGGGCATTAGGGGGCGGTCAGAAGTGTCCTCTCCATAGGTCACCAGCAG
+
FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576079_2.fastq <==
@SRR6576079.1 1/2
NTATANTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGC
+
#FFFF#FFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8FFFFFFFFFFFF8FF
@SRR6576079.2 2/2
GTTTCCTTTTGTTCTAGAGCTTTTAGGTGTGCTGTCAAGCTGCTAGCATATGCTCTCTCTAGTTTCTTTTTGATGGCAGTCAGAGCTATGAGTTTTTCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576079.3 3/2
TCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGT
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576079.4 4/2
CCTCTTATCTACCTGTAATTCTGACAGGATTAGGTGGACAAATGACATTCATAGAGAGGATAAAAAATATGATATGCATTCTTAATTTTGACTTTTGGTT
+
FF-FFFFF-8FF8FFFFF-8F8F8F--FF-F-FF-F-F-FFFFFF-FF-FFF-FFFFFFFFFFFFF-FFFF-FFFFFFF-F---FFF-FFF8---FFFF-
@SRR6576079.5 5/2
GCCATGGGGCTGCTGGTTGGAGATGACTTATGGGCTGTGGTCATATTCACAGCCATCTTCCTGCTTCTGGTGGACCTGGTGCACCGGCGCCAGCGCTGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576079_1.fastq

Printing command:
fastqc --outdir SRR6576079_1.fastq

Analysis complete for SRR6576079_1.fastq

Processing SRR6576079_2.fastq

Printing command:
fastqc --outdir SRR6576079_2.fastq

Analysis complete for SRR6576079_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 760M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 46 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 380M Oct 12 19:46 SRR6576079_1.fastq
-rw-r--r--   1 kkarri waxmanlab 380M Oct 12 19:46 SRR6576079_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:49 EDT 2018
0 hours, 0 minutes and 40 seconds elapsed.
==========================================================