-----------------------
Start of variable list:
-----------------------
Sample_ID:
C3-MAA100041-3_9_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 19:44:28 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791023
Current job name : Step_02_C3-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791023.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C3-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:44 SRR6575362_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:44 SRR6575362_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575362_1.fastq <==
@SRR6575362.1 1/1
GTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTTTGGGGCTGACCCTAGTGTGTGTCCATGCAGAAGAAGCTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575362.2 2/1
CATCAATAAATGGAGACGTATAGGAAAAGTCAGACTACGTCTACAAAATGTCAGTATCATGCTGCGGCTTCAAATCCGAAGTGATGTTTTGATGTGAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575362.3 3/1
ATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575362.4 4/1
GTACATGGGGAGTGTAGCCACGATCACAAGAAAGACTTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTGTG
+
-FFFFFFF-FFFF-FF-FF8F8F8FFFFFFFFFFFF8FFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF--FFFF
@SRR6575362.5 5/1
CTGTGAAGGTTCCCATGATGAAAATGAAGTTACTGACTGCACGCCACTTCCGTGATGAGGAGCTATCGTGCTCTGTGTTGGAGCTGAAGTACACAGGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575362_2.fastq <==
@SRR6575362.1 1/2
CAGTATGGACTTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTATCTTCTATCTTTTCTCTCTTGTCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575362.2 2/2
CATTCTAGCCTCGTACCAACACATGATCTAGGATGCTGCTGACCTCCAACAGGAATTTCACCACTTAACCCTCTAGAAGTCCCACTACTTAATACTTCAG
+
FFFFFFF-FFFFF8FFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FF--FFFFFFFF-FFFF-FFFFFFFFFFFFF8FF88-
@SRR6575362.3 3/2
CTGTAAGAGATGAAGAGTGCTCGGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6575362.4 4/2
ATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGATTTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTATC
+
FFFFFFFFF8FFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF8FFFFFF-FFFFFFFFFF8F-
@SRR6575362.5 5/2
ACACACAGCTGGTAATACGGCCTTACGAATGCCACCAATAACCCCTGTGGCAGCAGCTGCTTCTGTGCCTGTCTCAGCCACATCCAGCACAGCCTTGTGG
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF8FFFF

Starting FASTQC command


Processing SRR6575362_1.fastq

Printing command:
fastqc --outdir SRR6575362_1.fastq

Analysis complete for SRR6575362_1.fastq

Processing SRR6575362_2.fastq

Printing command:
fastqc --outdir SRR6575362_2.fastq

Analysis complete for SRR6575362_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 335M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C3-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 168M Oct 12 19:44 SRR6575362_1.fastq
-rw-r--r--   1 kkarri waxmanlab 168M Oct 12 19:44 SRR6575362_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:07 EDT 2018
0 hours, 0 minutes and 39 seconds elapsed.
==========================================================