-----------------------
Start of variable list:
-----------------------
Sample_ID:
A2-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 19:42:18 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790923
Current job name : Step_02_A2-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/8790923.1.linga

Loading required modules...


List files in scratch directory:

total 81M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:42 SRR6576994_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:42 SRR6576994_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576994_1.fastq <==
@SRR6576994.1 1/1
CCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576994.2 2/1
ACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCC
+
FFF8FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF8-FFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFF-FFFFFFFF-FFFFF-FF-FFF
@SRR6576994.3 3/1
GCGCAGCTCTTGTCAAAGCTCAGGATCCCAGCTGCGTACCAGGTGTCCTCCTCCATGTCATGAATGGCAAAGGCACTGCCGGCGTCACCGTAGCAGGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576994.4 4/1
GTTGTGTCCTACGGGATGTACATTGCAACAAACGTTGTTAAACCAGGAAAGGCCAATCAAGAGTAGTATTGCTGAGTTAAATAACAACATACAGTCTGTT
+
--FFFFFFFFFFF-FFFFFFFFFFF8FFFFFFFFFFFFFFFF8FFFFFFFFF-FFF-FFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFF-FFFFF
@SRR6576994.5 5/1
ATACTACTAACAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACC
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576994_2.fastq <==
@SRR6576994.1 1/2
GATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576994.2 2/2
GTGCAAGGGTAATCATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTGTCTAGGGTGTAACAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGA
+
F-FFFFFFF8FFF8FFF--FF8FFF-F-FF-FFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFFF-FFFF-FFFFF-FFFFFFFF---FFF-FFFFFF--
@SRR6576994.3 3/2
ACTTTAGATTTACCGATCGTCTCAAGTATGTCATGCTGCCTGTGGCCGACCAGGACAAGTGTGTGGTGCACTATGAGAATAGTACAGTGCCCGAGAAGAA
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576994.4 4/2
GATGAGATACATTTCGGAAGTCTCACCTCCCTTCCTAATGATCTCCTCACACTCTTTCCCAGACACCACTGGAATGTTGCAGCTGACAGTGCATGGAGTG
+
-FFFFFFFFFF-8FFFFF-FFFFFFFF-FFFFFFF-FFFFFFF-F-FFFF-FFFFFF-FF---FFFFFFFFFFFFF--F-FFFF-FFFF-F-FFF-FF--
@SRR6576994.5 5/2
GTAGTAAGTAACTACATGTGAAATAATTCCAAATCCTGGGAGGATAAGAATATAAACTTCTGGGTGCCCAAAGAATCAGAACAGATGCTGGTAGAGAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8FF

Starting FASTQC command


Processing SRR6576994_1.fastq

Printing command:
fastqc --outdir SRR6576994_1.fastq

Analysis complete for SRR6576994_1.fastq

Processing SRR6576994_2.fastq

Printing command:
fastqc --outdir SRR6576994_2.fastq

Analysis complete for SRR6576994_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 428M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 A2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 214M Oct 12 19:42 SRR6576994_1.fastq
-rw-r--r--   1 kkarri waxmanlab 214M Oct 12 19:42 SRR6576994_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:00 EDT 2018
0 hours, 0 minutes and 42 seconds elapsed.
==========================================================