-----------------------
Start of variable list:
-----------------------
Sample_ID:
F3-MAA100040-3_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 19:44:29 EDT 2018
Running on node : scc-yf2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791156
Current job name : Step_02_F3-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791156.1.y

Loading required modules...


List files in scratch directory:

total 61M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:44 SRR6575229_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:44 SRR6575229_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575229_1.fastq <==
@SRR6575229.1 1/1
GAAATAGTCACTGTACTTGAACTTCCCATTTTCATTCAGAAAATGCTCAGGTTTAAATGTCTCTGGATCTGGAAACTCATAGTTGTCAAATAAAAGGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575229.2 2/1
CCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCC
+
8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575229.3 3/1
GCGCTAAATATCCTGGTGTTGCTGGGCCTGTGCTGGTCCCTGGCTGTTGCCAGCCCTCTTCCTACTGCCAACGGGAGAGTTGCCGAAGTTGAAAATGGGA
+
FFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575229.4 4/1
TAGGAACACTGAAGATGCTCTCTGGGGAAACATTGTATATCTCTCATGTGTGTATCCCACAAGGGTTTCAGAACTGAGTTACTCTTGCAGTAGTAACTGC
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6575229.5 5/1
GCTCTGGGTTGCCAGACTACTCACTCCAACCATGAGGTGCTGCAAAACTGCCCACTTGTCATCTTTGCCACCAAACCCCAAGTCCTGCCAACTGTCCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575229_2.fastq <==
@SRR6575229.1 1/2
CAGCACAACTCTGAGATATGGGCTCCTGATTCTCATGAAATACCCAGAAATTGAAGAGAAACTTCATGAAGAAATTGACAGGGTTATTGGGCCAAGCCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575229.2 2/2
CTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575229.3 3/2
GTCCCATTGTGATCCATGGTCGCAGCATCAAAGCTCCAGGTATCCAAGCAGTGTTCGGGTACATCTGAATCTGGCTTGGTCCCATTTTCAACTTCGGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575229.4 4/2
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTAAACATACAATTTTTTTTTTTTTTACCAAGAAAAAAAAAAGAGTTTA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF----F------------FF----FF-F-F-------------F------8-F
@SRR6575229.5 5/2
TAGATTGGGAGAGACTCGCAATACTCGTGTGTTCGGGGGTAACAGCCCCTCCATTGTGCTCAGAGAGATCCCAGCAGCCACAGATACGATGATGTGCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575229_1.fastq

Printing command:
fastqc --outdir SRR6575229_1.fastq

Analysis complete for SRR6575229_1.fastq

Processing SRR6575229_2.fastq

Printing command:
fastqc --outdir SRR6575229_2.fastq

Analysis complete for SRR6575229_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 345M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 173M Oct 12 19:44 SRR6575229_1.fastq
-rw-r--r--   1 kkarri waxmanlab 173M Oct 12 19:44 SRR6575229_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:54 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================