-----------------------
Start of variable list:
-----------------------
Sample_ID:
E1-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-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791107
Current job name : Step_02_E1-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/8791107.1.linga

Loading required modules...


List files in scratch directory:

total 75M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 43 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:44 SRR6576042_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:44 SRR6576042_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576042_1.fastq <==
@SRR6576042.1 1/1
ANCCAAGATAGTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCTGGTCGTCTAC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576042.2 2/1
GNACCAAGAAATACCTTGAGGAGCGGCTGATAGAGCTGCTCAGGGACAAAGATGCTCTCTGGCAAAAATCCGATGCACTGGNATTCCAGCAGAAGCTCAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6576042.3 3/1
CTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576042.4 4/1
GCCATGCAGAGTTTCCGCTCCAGCCCCTCCTTGGTGCAACACTCAGGAGTTCCAGGGTGAACCGGAAAGGGAGCATCACTTTCACAGGACTTAACAGACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576042.5 5/1
CTTCTCAATAACATCCGCTCCTAAGGCAACAGAAACTACTGGGGCGAGTATTCCCAATGTATGGTCAGAATATCCCACAGGGATATTGAATATACTTTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576042_2.fastq <==
@SRR6576042.1 1/2
NCTTGNATTCTGAGCCCGGGCATCGCCCCTCGTTTATGAACTAGCCTATCGCAGACGGTATCAACAGGAACATCCTCGTGTTAGATATTGAGGCTGCTTC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576042.2 2/2
NCCCTNGCTAGTGNCTGAACCACTGCTATCATTGGATCCAGAGCCTTCGCCGAACTTCTGGAAGCAGGCTCGGCAGCAGCGTTCCTTCTTGCCACTGGGC
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576042.3 3/2
NGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCC
+
#FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6576042.4 4/2
NTACATGGGGCCTTTTGCGTGGTGGCCGGCAGGTGAGAGGAGGTGCTGCAAGACTCTCTGGTCGCAGAATGAAGAGGGTTCTGGTTCTCCTGCTGGCCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576042.5 5/2
CTACAGGAATGTCTGATATTGGGGAAATTTGGGAAGCAGTTAAAGTTTTAGAAAATAATGGATGCAGGGATATTATTTTATTGCATTGTATTTCATCTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576042_1.fastq

Printing command:
fastqc --outdir SRR6576042_1.fastq

Analysis complete for SRR6576042_1.fastq

Processing SRR6576042_2.fastq

Printing command:
fastqc --outdir SRR6576042_2.fastq

Analysis complete for SRR6576042_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 443M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 43 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 222M Oct 12 19:44 SRR6576042_1.fastq
-rw-r--r--   1 kkarri waxmanlab 222M Oct 12 19:44 SRR6576042_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:56 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================