-----------------------
Start of variable list:
-----------------------
Sample_ID:
L5-MAA000907-3_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 19:41:28 EDT 2018
Running on node : scc-yh4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790851
Current job name : Step_02_L5-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790851.1.y

Loading required modules...


List files in scratch directory:

total 28M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 29 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576554_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576554_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576554_1.fastq <==
@SRR6576554.1 1/1
CCCTGGGCTGGTGGTCCTAAGGTCTAAGAAAGCAGACTGTGAAAGCCTTAAGGAGGAAGCCAGTAAGCACCACGCCTCCATGGCATCTGCATTAGTTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576554.2 2/1
CTGTATGTATGCCTCACCATTTTGTTAGTCAGTAAGTAGATGTAAATACATGAATTTGTAGTTTCTTCTATCACTTTTCTCCTAGTTTGAATCTTTTTTT
+
FFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576554.3 3/1
GGTGGTATCAATCTAAAAGATGCCACTTCCAAGGTAGCGTTGGTATATGGACAGATGAACGAACCACCTGGCGCTCGAGCCCGGGTAGCTCATACTGGTT
+
--F---FFFFFFFFFFFF8FFFFFFFFFFFFF8FFFFFFFF-8FFFFF-F-FF-FF--FF--FF--FFFFF---FF-F-FF--F-FFFFFF--FFFFFFF
@SRR6576554.4 4/1
GCGGCGGACATGGCGGCGCTGATCACCAAACACAAGTGGGAGCAGGCTGGTGAAGCAGAGAGACTCAGGGCCTACCTGGAGGGCACGTGCGTGGAGTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576554.5 5/1
GGCAGCACGGGACAGACAGCCCCTTACTATGCTACCTCGACCGTGGAAGTAATTTTCCACGTTTCCACTCGGATGCCATCAGATTCAGATGATTCTCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576554_2.fastq <==
@SRR6576554.1 1/2
ACATTTGGCTGCTAAATCTAAAAGGCCTGGGTTTGATCCCTAAGACACACATGGCAGGAGACAACTGGTTCCCATATGACTCTTCTTATCCTGTCCTAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576554.2 2/2
GTCTATATGAGGAAGACAACATGAGTGAATTCCTGAAACTCAAACAGGAGTTTCTATGATGAAAATTGTACCCAATATGTCAGGGTTAAAAGTGACATGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576554.3 3/2
CCCTTCTTGGTGGTGGTGAAACTTTCCTTCATTGTGCCCATGTCGGTGACTATGGAGGGCTTGTAGCCTACAGCAGACGGGATTCTTCCCAATAAGGCAG
+
-F--FF-FFF8-8FF-FFF88F-FF--F--FF--F-FF--F--------FFF--F-F-----F-FFFF-F-F-FFFF-FFFFFF-F-FFFF--FF8FFF-
@SRR6576554.4 4/2
GCCCCTGATGGTACACATGGCATGTGTAATACTGCTCCTTCCCAAGAGGCACCACCACAGATGCCCACTTCTGGAAGGTTCCATCCCCTGCAGGCCTGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFF8F
@SRR6576554.5 5/2
CCATCGAACAGGGGCCCAAAGAATGGAACCTCAGGCTTCTTCGTTATCGTGATAAAGAACATATGATTCTTCATTGGGTAAATAATGATGGAAACGTCTC
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576554_1.fastq

Printing command:
fastqc --outdir SRR6576554_1.fastq

Analysis complete for SRR6576554_1.fastq

Processing SRR6576554_2.fastq

Printing command:
fastqc --outdir SRR6576554_2.fastq

Analysis complete for SRR6576554_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 144M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 29 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  72M Oct 12 19:41 SRR6576554_1.fastq
-rw-r--r--   1 kkarri waxmanlab  72M Oct 12 19:41 SRR6576554_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:40 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================