-----------------------
Start of variable list:
-----------------------
Sample_ID:
A1-MAA100039-3_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 19:42:18 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790919
Current job name : Step_02_A1-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790919.1.linga

Loading required modules...


List files in scratch directory:

total 86M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  42M Oct 12 19:42 SRR6576785_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  44M Oct 12 19:42 SRR6576785_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576785_1.fastq <==
@SRR6576785.1 1/1
TCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576785.2 2/1
TGCCACCACCACCCGGCTTCAAAGTGAATTTTAATAAGATGTTTCTGGCTTAATTTTTAAAATTGTGTCAAGCACTTGTGTTTTTGAATCTACCACTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576785.3 3/1
GTCCAAAGACCATCCACAAAGTCAACGTGCAGGGCACACAGAATGTGATTGATGCTTGTGTGCAGACTGGCACTCAGTACCTGGTCTACACGAGCAGCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576785.4 4/1
GCTATCACCATTGAAGCTTCGGCTTCTACATTCTCCTGTTTCCAAGGGCCCTTGTTGAACTCCTTCTCTCGAAGAGACACCTCATAGGTTTTCACATGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFF8FFFF--FFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFF-F-F-FFFFF-FFFFFFFF
@SRR6576785.5 5/1
ACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576785_2.fastq <==
@SRR6576785.1 1/2
NTATCAACGCAGAGTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576785.2 2/2
NTATTAGCATGTATGAGACTGATTAGCAAAAGTGTATAAGAATGGCTAGGAAGTGATCCCACAGAAGAAAATCCACAAGGTGGGAATGCTTTATTCCTCT
+
#FFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8FFFFF
@SRR6576785.3 3/2
NCATAAATGCCCGTGGGTCGAAGGGCACATGTCACCAGGGGTAGCCCTCCATTGACCTTCCTTCCATTGGCCTCGAGGACCAGCTGCTCAGCAAGGGCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576785.4 4/2
ACGCAGAGTACATGGGAGTCTCTTCGCTCGCGCCCGTCTCTCTATCGTCGCTCTAGGCGCCCCACGGGCCAACCCAAGGCGTCAATATGTCGTACAACTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-F--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFF-F-FF-FFFFFFF-F----FF8FFF
@SRR6576785.5 5/2
ACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF8FFFF

Starting FASTQC command


Processing SRR6576785_1.fastq

Printing command:
fastqc --outdir SRR6576785_1.fastq

Analysis complete for SRR6576785_1.fastq

Processing SRR6576785_2.fastq

Printing command:
fastqc --outdir SRR6576785_2.fastq

Analysis complete for SRR6576785_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 511M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 A1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 256M Oct 12 19:42 SRR6576785_1.fastq
-rw-r--r--    1 kkarri waxmanlab 256M Oct 12 19:42 SRR6576785_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:05 EDT 2018
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================