-----------------------
Start of variable list:
-----------------------
Sample_ID:
M8-MAA000907-3_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 19:49:49 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791389
Current job name : Step_02_M8-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791389.1.linga

Loading required modules...


List files in scratch directory:

total 17M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 82 root   root       84K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 M8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 8.0M Oct 12 19:49 SRR6576608_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 8.6M Oct 12 19:49 SRR6576608_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576608_1.fastq <==
@SRR6576608.1 1/1
CGACCTATCGGGACAGCCAGGCCTACCAGGCCTACAAGTCCGGCGATGCCGATCTCGCCGCCAAGCAGAGCGGCCTCACGGTCACGCCGGAGGCAGCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576608.2 2/1
CGACCTATCGGGACAGCCAGGCCTACCAGGCCTACAAGTCCGGCGATGCCGATCTCGCCGCCAAGCAGAGCGGCCTCACGGTCACGCCGGAGGCAGCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576608.3 3/1
CGGTAACTGTGCTTGCCATTAAACCTGGAAGACTGGTTCGGTCTCAGAAGCCCACATGGAAGTAGAGAACCAGAAAACTCCTACAAGCTGTCTCTGTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576608.4 4/1
CTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGTATCCCGGAAGCTGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFF-FFF
@SRR6576608.5 5/1
CTTCTTAGAGGGACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576608_2.fastq <==
@SRR6576608.1 1/2
GCATGGGAGCGATCGCCGCGCGCAATGGCGTCGACCTCGTTGAACATGTCGTCCACGAGGATCTGCGACATGCGCGAGGTGATGTCGCCCTTCTCGGTCA
+
8FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576608.2 2/2
GCATGGGAGCGATCGCCGCGCGCAATGGCGTCGACCTCGTTGAACATGTCGTCCACGAGGATCTGCGACATGCGCGAGGTGATGTCGCCCTTCTCGGTCA
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576608.3 3/2
TTCTAATTCAGGGGGCAAGGATAATCTTAAAGACTAAATCATTCTTTTCTTTGAATATCTGAGGCCACAATAAGAATAGTCTTTCTCCTAAAGTTAAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFF-F-FFFFF8FF
@SRR6576608.4 4/2
GTTCAAAGCAGGCCCGAGTCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAA
+
8F-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFF--FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-FFF
@SRR6576608.5 5/2
GAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFF

Starting FASTQC command


Processing SRR6576608_1.fastq

Printing command:
fastqc --outdir SRR6576608_1.fastq

Analysis complete for SRR6576608_1.fastq

Processing SRR6576608_2.fastq

Printing command:
fastqc --outdir SRR6576608_2.fastq

Analysis complete for SRR6576608_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 87M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 82 root   root       84K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 M8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:49 SRR6576608_1.fastq
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:49 SRR6576608_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:09 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================