-----------------------
Start of variable list:
-----------------------
Sample_ID:
F8-MAA100138-3_56_F-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 19:46:08 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791178
Current job name : Step_02_F8-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791178.1.linga

Loading required modules...


List files in scratch directory:

total 106M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:46 SRR6575871_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:46 SRR6575871_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575871_1.fastq <==
@SRR6575871.1 1/1
ATTTCCATGCTTGCATCGAAGACGTTGAATGTAAAGCCCTTAGTTACCCACAGATTCCCCCTGGAGAAGGCAGTTGAAGCCTTTGAAACAGCCAAAAAGG
+
FFFFFF-FFFFFFFFFFFFFFFFFFFF8FFFFFFFF8FFFFFFFFFF--FFFF-FFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575871.2 2/1
GGCCACATCTGTCATAGATGAGGAAGTCATCTTTGTTTCCATTTAAGAGAGTCCAGACATCTATGCCATCTTCTTCTTGTCTGTACACTGCGATGTGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575871.3 3/1
GAGCCGGTTTCTCCTCAAGGTTCATTAAACTGCTGAAGAAGTTCACCAGACTAGTTCCTGCTGACCTGACAAGGGGTGTCAGCTGCTCGTGTGTCTTCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575871.4 4/1
CTACAACACTATACAGCAACATAGACCTGATCAGGGTTCTTTAGCCAATATGCCCAACCTGGATGCTGTGGCGCTGAAGGCTGCAATGGCTCAGTTTGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575871.5 5/1
TCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575871_2.fastq <==
@SRR6575871.1 1/2
NCTTAGTAGCTGAGACAGAGGTAGTCTTTGGGCAGAGCCGAGTGCCCTTATACTTTCCACATCTGTGGAATGTAAGCTAGGGTACCTCATCTGGGATTGA
+
#-F-F--FFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFF-FFF--FFFF-FFF8F-FF-FFFFF--FFFF-F-F
@SRR6575871.2 2/2
NTACATAGGAGATCAAAATCCAATGCTAAACTCAGAGGGCAAAGTGACAGTGGTTGCTCTTCTTCAAGCCAGCTGATACTTGTGTCTTCTGCAGGCATCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF-FFFFFF
@SRR6575871.3 3/2
NCTGGTCACCATCTGTAGCCTGGAAGGAGCTTTGGTTAAGAGACAGGCAGACGGACCGGATATGCAGAGCCTGTTCACTCAATACTTTCAGAGCATGACT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575871.4 4/2
CTGCAAATGCCATCGACATCATCAAGAGAGCAGTGTCTTCACCTGCTCAGGTGACCTATGAAGGATGCTCTCTGGATCTTTGTATGCGTTGTCTGGAGTC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF-FF
@SRR6575871.5 5/2
CCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FF-FFFFFFF-FFFFF-FFFFFF

Starting FASTQC command


Processing SRR6575871_1.fastq

Printing command:
fastqc --outdir SRR6575871_1.fastq

Analysis complete for SRR6575871_1.fastq

Processing SRR6575871_2.fastq

Printing command:
fastqc --outdir SRR6575871_2.fastq

Analysis complete for SRR6575871_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 577M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 289M Oct 12 19:46 SRR6575871_1.fastq
-rw-r--r--   1 kkarri waxmanlab 289M Oct 12 19:46 SRR6575871_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:39 EDT 2018
0 hours, 0 minutes and 31 seconds elapsed.
==========================================================