-----------------------
Start of variable list:
-----------------------
Sample_ID:
B3-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 19:42:20 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790973
Current job name : Step_02_B3-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/8790973.1.linga

Loading required modules...


List files in scratch directory:

total 105M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:42 SRR6576816_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  54M Oct 12 19:42 SRR6576816_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576816_1.fastq <==
@SRR6576816.1 1/1
GNGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCATCCTTTTCGTTAATGAGATGAGC
+
F#F8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576816.2 2/1
CACACACCTGGTGTGGCAGCAGATCTGAGTCACATTGAGACCAGAGCAAATGTGAAAGGCTACCTTGGACCGGAGCAGTTGCCAGATTGCCTCAAAGGTT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576816.3 3/1
CTCAAAGAGATACTCGCCCAGAGACCCCTGGGGCGCGCCAGTCTGCGCTGGTTGTGGCCCCGCCACCCTGCGGAGGTTGGTCAGATGGTTGCCCATCTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576816.4 4/1
CTGCTGGCCCCATACGCCAAGGGTGGGAAAATCGGACTCTTTGGAGGTGCTGGCGTTGGAAAGACAGTACTGATCATGGAGCTAATCAACAATGTCGCCA
+
FFFFF--FFFFFFFFFFFF88888F8FF8F8FF8FFFFFFFFFFFF-F-FF--FF---FFFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFF-F-FF--FF
@SRR6576816.5 5/1
CTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTTCCTATCCATACAGCATCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576816_2.fastq <==
@SRR6576816.1 1/2
NTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576816.2 2/2
GTACACACCGTGCTTCTTGAAAACTTCTGCTGTGATGGGGATGGTGGAGTTCACTGGGTTGGCAATGATGCACACCATGGCTTCAGGACAGTGCTGGGCA
+
FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFF--FFFFFFFFFFFFFFFF-FFFFFFFFF8
@SRR6576816.3 3/2
CTCTTCCAGGATGTGCAGAAGCCATCTCAAGATGAATGGGGTAAAACCCAGGAGGCCATGGAAGCTGCCTTGGCCATGGAGAAGAACCTGAATCAGGCCC
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576816.4 4/2
CAATAAGGCAGACACATCAGAGCAATACATCGTAAAGCTGAAGATGTTGAAAATAAACAGAATCACAACAAGCCCCTCCTCCTCTCAGAAGAATTCAGCA
+
FF-FFF-F-FFFFFF-FF-888-8FF-FF--FF-FFFF-FFF-FF-F-F--FFFFF--FF-F----FF-----FF-FFFFF--FFFFFF-FF-FF-8--8
@SRR6576816.5 5/2
ATCATTTATTGAACAGGAAGAGGAAGAATTTCATGAAAAATTGTCAAGGGTGTATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF8F

Starting FASTQC command


Processing SRR6576816_1.fastq

Printing command:
fastqc --outdir SRR6576816_1.fastq

Analysis complete for SRR6576816_1.fastq

Processing SRR6576816_2.fastq

Printing command:
fastqc --outdir SRR6576816_2.fastq

Analysis complete for SRR6576816_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 608M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 B3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 304M Oct 12 19:42 SRR6576816_1.fastq
-rw-r--r--   1 kkarri waxmanlab 304M Oct 12 19:42 SRR6576816_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:15 EDT 2018
0 hours, 0 minutes and 56 seconds elapsed.
==========================================================