-----------------------
Start of variable list:
-----------------------
Sample_ID:
F1-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 19:44:29 EDT 2018
Running on node : scc-ye1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791147
Current job name : Step_02_F1-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/8791147.1.y

Loading required modules...


List files in scratch directory:

total 85M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:44 SRR6576916_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:44 SRR6576916_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576916_1.fastq <==
@SRR6576916.1 1/1
GTATCAACGCAGAGTACATGGGGAGTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576916.2 2/1
CTCACCAGGACTCCACCATCATCCCTTCCTATCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCATCCTGTCTCACTGAGAAGTCCAATTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576916.3 3/1
GGGTGGGAAGACTGGGCCTGGCACATCTCACTTAGCCGCAGGAGCCGGTTTCTCCTCAAGGTTCATTAAACTGCTGAAGAAGTTCACCAGACTAGTTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576916.4 4/1
GTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576916.5 5/1
GTCTGTACCCGTAGAGCAAATGCAGACTGCTGATTATCCAAGTGCATGTTGTATCTCAGTGTAGTCTGAGCATACACACATCCATCACCTGATACACTGA
+
-FFFFFF-F----FFF-FFFF8F8F8FFF8F8888-F8FFFFFF-FFFFF-FFF-FFFF--FF-FFFF-FFFFFFFFF-F-FF--F-F-F-FFF-FF---

==> SRR6576916_2.fastq <==
@SRR6576916.1 1/2
NTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGAGTGGCATTGGATAGGTCAATGATATTTT
+
#-FFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFF-FF-FFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576916.2 2/2
NTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATGGTAAAAATTTTTTTAAAAGGAAAAGTAAAAAATAAATTAAAAATTTTAATGGGTATAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-----FF----F--FFF-F-F---------F-FFF--FF--FFFFF-FF--F--F--F----FF8
@SRR6576916.3 3/2
GTATCAACGCAGAGTACATGGGGCAGCACAGAATCGCACTGTTCCTAGGCCATAGTCTGCCATCATGAAGCTGCTCGCAATGGTCGCACTGCTGGTCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576916.4 4/2
ATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576916.5 5/2
GTAATTGCCTGTTACTTCAGCAGGTCCCATTACCAGACATTCCTGGGGAATATACCATCAGTGTATCAGGGGAAGGATGTGTGTATGCTCAGACTACACT
+
8-FFFFFFFFFFFFFFFFFF8FFFF-FFFFFFF-FFFFFFFF-FFFFFF-FFFFF-FF-F-FF-FF-FFFFF-FFFFF-FFF-FFFFFFFFFFFF-FFFF

Starting FASTQC command


Processing SRR6576916_1.fastq

Printing command:
fastqc --outdir SRR6576916_1.fastq

Analysis complete for SRR6576916_1.fastq

Processing SRR6576916_2.fastq

Printing command:
fastqc --outdir SRR6576916_2.fastq

Analysis complete for SRR6576916_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 514M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 257M Oct 12 19:44 SRR6576916_1.fastq
-rw-r--r--   1 kkarri waxmanlab 257M Oct 12 19:44 SRR6576916_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:53 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================