-----------------------
Start of variable list:
-----------------------
Sample_ID:
C8-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 19:44:28 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791041
Current job name : Step_02_C8-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/8791041.1.linga

Loading required modules...


List files in scratch directory:

total 58M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6576854_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:44 SRR6576854_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576854_1.fastq <==
@SRR6576854.1 1/1
CCTAGTAACATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAGACACGATGGAAAGCAGATCACAGAACTTCTTACTGGATGCTGTATGGATAGGAAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576854.2 2/1
CACCAGGAGGAGACAAGCAGGCTCTTCAGGGGCAGAGTTTCTTGCCCGAAGAGGGCAAGCTCAGAGCCTTACTTGAAGGAGGCCCTCACCACCCTGCCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576854.3 3/1
GGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576854.4 4/1
CCTAGTAACATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAGACACGATGGAAAGCAGATCACAGAACTTCTTACTGGATGCTGTATGGATAGGAAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576854.5 5/1
ACTTAATTCTGTACTCCATTCTTGCTTAGTCGTATTAGCCATAAAAGAGGTCAGGTTCATAGGACTTAGTTTCTCTATGAAACCATCATTGATTATGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576854_2.fastq <==
@SRR6576854.1 1/2
NTTCATCTCATTAACAAAAAGGATGGAGAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAAGTTTGCAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6576854.2 2/2
NAGTGCATTGTGTGGCTGCTGCTCAAAGAGCCCATGACTGTGAGCTCAGACCAGATGGCCAAGCTGCGCAGCCTCTTCTCCAGCGCAGAGAATGAGCCCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576854.3 3/2
NTCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576854.4 4/2
ATTCATCTCATTAACAAAAAGGATGGAGAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAAGTTTGCAC
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576854.5 5/2
GTACATGGGAACAGATTACACTTTAAATATCTACTCATCATTTTCTCTCTCAGAGTCCTAGCTTGAGTTGCACTGCATGTATCTGTGCATCTTGTTCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF88FFFF

Starting FASTQC command


Processing SRR6576854_1.fastq

Printing command:
fastqc --outdir SRR6576854_1.fastq

Analysis complete for SRR6576854_1.fastq

Processing SRR6576854_2.fastq

Printing command:
fastqc --outdir SRR6576854_2.fastq

Analysis complete for SRR6576854_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 425M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6576854_1.fastq
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6576854_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:12 EDT 2018
0 hours, 0 minutes and 44 seconds elapsed.
==========================================================