-----------------------
Start of variable list:
-----------------------
Sample_ID:
O9-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 19:46:09 EDT 2018
Running on node : scc-wl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791299
Current job name : Step_02_O9-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/8791299.1.w

Loading required modules...


List files in scratch directory:

total 20M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 36 root   root       12K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 O9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.6M Oct 12 19:46 SRR6576705_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.9M Oct 12 19:46 SRR6576705_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576705_1.fastq <==
@SRR6576705.1 1/1
CCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGA
+
-FF-FFFF--FFFF8--FFFF8FFF8F8F88FFFF-F8FFFFFFFFFFFF-FF-FFFF-FFFFFFFFFFFFFFFF-FFF-FFF-FFFFFFFFFF-FFFFF
@SRR6576705.2 2/1
GAGTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGC
+
FFFFF8F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576705.3 3/1
TAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576705.4 4/1
CCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576705.5 5/1
CCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTT
+
FFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-

==> SRR6576705_2.fastq <==
@SRR6576705.1 1/2
NTGTGGTAATTCTAGAGCTAATACATGCCGACGTGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTTCATTTATCAGATCAAAAAAAACCCGTTTAGCTC
+
#F-F-FFF-8FFFF8FFFFFFFFFF--FF-FFF--FFFF-FFFFF-F-FFFF-F-FF---F---F---FF--F-FF-F-FFFFF--FF-F-8-F-F-FF-
@SRR6576705.2 2/2
GCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGATCCGCCCGCCCGCTCCCAAGATCCAACTACGAGCTTTTTAACTGCAGCAACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFF-F-FFFF-FFFFFF-F8FFFFFFF-FFF-FFF
@SRR6576705.3 3/2
CTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576705.4 4/2
AAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6576705.5 5/2
AAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTG
+
FFF-FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF8F

Starting FASTQC command


Processing SRR6576705_1.fastq

Printing command:
fastqc --outdir SRR6576705_1.fastq

Analysis complete for SRR6576705_1.fastq

Processing SRR6576705_2.fastq

Printing command:
fastqc --outdir SRR6576705_2.fastq

Analysis complete for SRR6576705_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 112M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 36 root   root       12K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 O9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:46 SRR6576705_1.fastq
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:46 SRR6576705_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:21 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================