-----------------------
Start of variable list:
-----------------------
Sample_ID:
D3-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 19:44:31 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791075
Current job name : Step_02_D3-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/8791075.1.linga

Loading required modules...


List files in scratch directory:

total 46M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D3-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:44 SRR6575389_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:44 SRR6575389_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575389_1.fastq <==
@SRR6575389.1 1/1
ACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575389.2 2/1
ACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575389.3 3/1
ATCATAGAGCTCCATCAGCTGGAAGGTTTCTCCATCCTTTTTGTTAATGAGATGAATCATAATATAATTATCATAGTCTGTCTTAAGTATAGTAAATGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575389.4 4/1
ATCCTGGGCAAAGCAACTGCACACACCTTCCCGCTGCAGAAGCGCGTACCCTCAGGGCTGCTCCCCAGGCTGCGGGCAGGGGACACTGCCTATGGCTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575389.5 5/1
AACGAGGGGCGATGCCCGGGCTCAGAATCCAAGGAGCAAAACTGCGTCGGTTTAGCTGAGATTGCACCGTTGTTATAATCGACCCGGGCTGCGACAATCG
+
FF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575389_2.fastq <==
@SRR6575389.1 1/2
ATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575389.2 2/2
GGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6575389.3 3/2
GTATACTATTATGCTGGCCACTGACAAAAGAGAAAAGATAGAAGAACATGGCAGCATGAGAGTTTTTGTCGAGTACATCCATGTCTTGGAGAATTCCTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575389.4 4/2
TCTCTAAGCACGGAAACCTTGGACACGTGAACATCAGCGCCATCCAGGAACCTCTCGCCGTTATTTTGCCTAAGAGAGAAACAGTTTTCTGTTTAGATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-F-F--FFFFFF-FFFFFFFFFFFF8FFFFFFFFFFFFF8F
@SRR6575389.5 5/2
GGACTTAAGCGCGGTGGCCTCCCCTATCCCCTACGAGGCTACCCGGATCGATGACGCGAATTGGGGACATTCAAATGAGCATCCTAGTCACCGCGTTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFF-FFFFFFFFFFF-FFFFFFFFFF

Starting FASTQC command


Processing SRR6575389_1.fastq

Printing command:
fastqc --outdir SRR6575389_1.fastq

Analysis complete for SRR6575389_1.fastq

Processing SRR6575389_2.fastq

Printing command:
fastqc --outdir SRR6575389_2.fastq

Analysis complete for SRR6575389_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 272M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D3-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 136M Oct 12 19:44 SRR6575389_1.fastq
-rw-r--r--   1 kkarri waxmanlab 136M Oct 12 19:44 SRR6575389_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:06 EDT 2018
0 hours, 0 minutes and 35 seconds elapsed.
==========================================================