-----------------------
Start of variable list:
-----------------------
Sample_ID:
C7-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 19:44:28 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791040
Current job name : Step_02_C7-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/8791040.1.linga

Loading required modules...


List files in scratch directory:

total 72M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 34 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:44 SRR6576001_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:44 SRR6576001_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576001_1.fastq <==
@SRR6576001.1 1/1
CNCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGNCGAGTCACCGCCCGTCCC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6576001.2 2/1
GCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576001.3 3/1
GTGGCCAGTGGAGCAGCTGGGGTGGGAAGACTGGGCCTGGCACATCTCACTTAGCCGCAGGAGCCGGTTTCTCCTCAAGGTTCATTAAACTGCTGAAGAA
+
-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576001.4 4/1
CTACAGTTCAACCTCACACAAACATCGGAGGCTGACATCCACAAGTCCTTCCAACACCTCCTCCAAACCCTCAACAGACCAGACAGTGAGCTGCAGCTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576001.5 5/1
ATACCACACACACCCTGGTGGAGAAGATCAACTACACTGGCCGTTTCTTACCTGGATTCGAGGCCCCAACATACAAGGATACCCTGCTTCCAAAACTACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576001_2.fastq <==
@SRR6576001.1 1/2
NAATANAACCGCGNTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGC
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576001.2 2/2
NAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576001.3 3/2
GTACATGGGGAGAGTAGACGGGAAGGACTGCAGCACAGAATCGCACTGTTCCTAGGCCATATTCTGCCATCATGAAGCTGCTCGCAATGGTCGCACTGCT
+
8-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFF-FF-FFFFF--F-FFF-FF-FFFFFFFF-FF-FFFFFF-8FF--FFFFFFFFF-F
@SRR6576001.4 4/2
CTGCAATGATGCACATCAAGCATGCCCGAGAGGGTCATCATGGGCACCTTCACTGTGGTGGACTCGTCCACATGGAACTCAGCTTCCTCAGTGTTCTCAG
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFF---FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576001.5 5/2
GCATGGGCTTGGTGAAGATCTGTAGGAGGTAGCCTTTCTCGTCATAGTCGACTAGGATATGCAGCTCCTCCAGGACGTCCATGCTCGCTTTCACCTGGAT
+
FF-FFFFFFFFF8FFFFFFFFFF8FFFFFF-FFFFFFFFFF-F---FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-F-F--FFFFF-F8--

Starting FASTQC command


Processing SRR6576001_1.fastq

Printing command:
fastqc --outdir SRR6576001_1.fastq

Analysis complete for SRR6576001_1.fastq

Processing SRR6576001_2.fastq

Printing command:
fastqc --outdir SRR6576001_2.fastq

Analysis complete for SRR6576001_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 394M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 34 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 197M Oct 12 19:44 SRR6576001_1.fastq
-rw-r--r--   1 kkarri waxmanlab 197M Oct 12 19:44 SRR6576001_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:52 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================