-----------------------
Start of variable list:
-----------------------
Sample_ID:
B5-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 19:42:19 EDT 2018
Running on node : scc-pc1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790985
Current job name : Step_02_B5-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/8790985.1.p

Loading required modules...


List files in scratch directory:

total 101M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 20 root   root       12K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:42 SRR6575971_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:42 SRR6575971_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575971_1.fastq <==
@SRR6575971.1 1/1
GAGCACGATAGCTCCTCATCACGGAAGTGGCGTGCAGTCAGTAACTTCATTTTCATCATGGGAACCTTCACAGATCTCTTCTCATCCAAGTAGAACTCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575971.2 2/1
GTACATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTC
+
FF8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575971.3 3/1
CCTCTGGCTTCGCCCTGCCCAGGCATAGTTCACCATCTTTCGGGTCCTAACGCGTACGCTCGTGCTCCACCTCCCCGGCGCGGCGGGCGAGACGGGCCGG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575971.4 4/1
GTCCTACAACAGTCTAGAAGACTTAAACAACAAGTACCTTTATATTGCAGTAACAGTCACAGAATCTTCAGGTGGATTTTCAGAAGAGGCAGAAATCCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575971.5 5/1
GTCCCTGTGGAATTTAAGGAGCATCATCTGAGCGAGGTGCAGAATATGGCTTCTGAGGAGAAGCTGGAGCAGGTGCTGAGTTCCATGAAGGAGAACAAAG
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575971_2.fastq <==
@SRR6575971.1 1/2
NTGAAGCAGACATCCACCAGGGCTTTGGCAACCTCCTACAGAGTCTCAGCCAGCCAGAAGACCAGGATCAGATAAACATAGGCAATGCCATGTTTATTGA
+
#FFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF--FFFFFF8FFFF-
@SRR6575971.2 2/2
NATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCTCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATG
+
#FFFF-F-FFFFFFFFFFFF8F-FFF--FFFF-FFFF-FFFFFFFFFFFFF-FFF-FFF-FFFFFFFFFFF-F-FFFFF-FFFF8FF-FF--FFF-FFFF
@SRR6575971.3 3/2
NAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCCGCCGCGCGTCGCGGCGTGGGACATGTGGCGTACGGAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF-FFFFFFFFFFFFFFF
@SRR6575971.4 4/2
CATCAGTGTCATGAGTGATGCTCCTCTTTGTTTCCAAGTCAGATGTCTCTTGATTCACATCGACTGTTTGTGCCATCAGAGTTACTGGGACCCCTCCTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575971.5 5/2
GTCGAACGCAAACTTTGCAATCCTCTGAGACTTGGTGCGAGTGACGATCTTCAGGCACTCAATGACACCCTTGGCGCTCTCATGTTCCAGAGAGCTATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575971_1.fastq

Printing command:
fastqc --outdir SRR6575971_1.fastq

Analysis complete for SRR6575971_1.fastq

Processing SRR6575971_2.fastq

Printing command:
fastqc --outdir SRR6575971_2.fastq

Analysis complete for SRR6575971_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 552M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 20 root   root       12K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 276M Oct 12 19:42 SRR6575971_1.fastq
-rw-r--r--   1 kkarri waxmanlab 276M Oct 12 19:42 SRR6575971_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:46 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================