-----------------------
Start of variable list:
-----------------------
Sample_ID:
F8-MAA100040-3_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 19:46:09 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791177
Current job name : Step_02_F8-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791177.1.linga

Loading required modules...


List files in scratch directory:

total 36M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:46 SRR6575240_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:46 SRR6575240_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575240_1.fastq <==
@SRR6575240.1 1/1
AATGAGATGAGCCATAAGAAAGTTATCATAGTCTGTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575240.2 2/1
ATCATAGGTGGATGCTCCGCCCACCACCAGTCCACCTCCATGGATCCACACCATCACTGGTAGTCTGCTGTTCTTTGTCAAGTCAGCAGGAGTGTAAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575240.3 3/1
AGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCTTAAATTCCATACTGTAAGAGATGAAGAGTG
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575240.4 4/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
-FFFFFFFFFFFFFFFF8FF8FFFFFFFFFFFFFFFFF8FFFF--FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575240.5 5/1
CTCGTGTCCTCTGCCGAAGAATTCCTGAAAGCTCTCTCTTGCATCACTGATTTTCTCAGCAGCCCAGACTCCCCCGGGACCCCTTTGGGCAGCATCATAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575240_2.fastq <==
@SRR6575240.1 1/2
ACCCTAGTGTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFF8FFFFF
@SRR6575240.2 2/2
GTGGTGAACACTGTTAAAGGCAAAGTCCTGGGGAAGTATGTCAATTTGGAAGGATTCACACAGCCTGTGGCTGTTTTCCTGGGAGTCCCCTTTGCCAAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575240.3 3/2
GAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGAT
+
FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575240.4 4/2
ACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTTCTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575240.5 5/2
AGCCTACACTGACATGAAGGAAGCTGGCTGGAAAGATGGAGACAAATACTTCCATGCTCGGGGGAACTATGATGCTGCCCAAAGGGGTCCCGGGGGAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575240_1.fastq

Printing command:
fastqc --outdir SRR6575240_1.fastq

Analysis complete for SRR6575240_1.fastq

Processing SRR6575240_2.fastq

Printing command:
fastqc --outdir SRR6575240_2.fastq

Analysis complete for SRR6575240_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 213M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 107M Oct 12 19:46 SRR6575240_1.fastq
-rw-r--r--   1 kkarri waxmanlab 107M Oct 12 19:46 SRR6575240_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:28 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================