-----------------------
Start of variable list:
-----------------------
Sample_ID:
E7-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 19:44:30 EDT 2018
Running on node : scc-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791126
Current job name : Step_02_E7-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/8791126.1.linga

Loading required modules...


List files in scratch directory:

total 63M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 35 root   root      132K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:44 SRR6575211_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6575211_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575211_1.fastq <==
@SRR6575211.1 1/1
GTTTGGAGAGAGAGCTTTTAAAGCATGGGCAGTAGCTCGTCTGAGCCAGACATTCCCCAATGCTGACTTTGCAGAAATCACCAAATTGGCAACAGACCTG
+
FF8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFF-FFFFFFFF-FFFFFFFFFFFFFFFFF-
@SRR6575211.2 2/1
GATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575211.3 3/1
GTATGTTATGGTGAATGCCAAGCTTGGAGAAGAATCAAAAGAACCTCTCTCTGATGAAGATGAGGAAGACAATGATGATGTTGAACCCATTTCTGAATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575211.4 4/1
TCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCAACCTTTTCGTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF--FFFFFFFFFFFF
@SRR6575211.5 5/1
GTCTTCCCTCTGTTTCTCACTGACACTACGTTTCTGCTATGGTCTGCGGTTGACGACCTCGATATGAGTTTTTGATTATTCGGTGGTTCCTTTTTTTTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF

==> SRR6575211_2.fastq <==
@SRR6575211.1 1/2
NTCAGCAACAGGGATACAGAGTAATCAGGGTGTCTTCTTGAATATTCATACAAGAACGTGCCCAGGAAGACATCCTTGGCCTCAGCATAGTTCTTGCACA
+
#FFFFFFFFFFFFFFFFFFFF8F8FF-FFFFFFFFFF-FFFFF-F-F-FFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575211.2 2/2
NGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575211.3 3/2
CCATCATAGTCGTCCGAGTCTTCATCCTCAGGGTCTGGATGCAAGGCCTGGCACTCACACATTGCTGTGAACATCGCCTCCAATGCTGACTTATCACTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575211.4 4/2
ATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTT
+
F8FFF-FFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FFFFFFFFFFFFF-FFFFFF-FFFFF-FF-FFFFFFFF-FFFFFFFF-8FFFF8-FF
@SRR6575211.5 5/2
CTTTCAGAGGCGGTGAGCTTCAACTCTGAGTCTCAAGTGTCACAGAGATTCAAAGTTCAGGGAGCTATCAGGTCACCCAAGAAAGAGCAAAGCACCTCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575211_1.fastq

Printing command:
fastqc --outdir SRR6575211_1.fastq

Analysis complete for SRR6575211_1.fastq

Processing SRR6575211_2.fastq

Printing command:
fastqc --outdir SRR6575211_2.fastq

Analysis complete for SRR6575211_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 348M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 35 root   root      132K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E7-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 174M Oct 12 19:44 SRR6575211_1.fastq
-rw-r--r--   1 kkarri waxmanlab 174M Oct 12 19:44 SRR6575211_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:53 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================