-----------------------
Start of variable list:
-----------------------
Sample_ID:
G4-MAA100042-3_9_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 19:41:28 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790789
Current job name : Step_02_G4-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790789.1.linga

Loading required modules...


List files in scratch directory:

total 263M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G4-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 116M Oct 12 19:41 SRR6575677_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 148M Oct 12 19:41 SRR6575677_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575677_1.fastq <==
@SRR6575677.1 1/1
ATGGTATACTATTATGCTGGCCACTGACAAAAGAGAAAAGATAGAAGAACATGGCAGCATGAGAGTTTTTGTCGAGTACATCCATGTCTTGGAGAATTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575677.2 2/1
CAAACACACCCATGTTACCTCTGGAAAGACACAGTCAAAAGCTTCTTGAAAACTACCATTCTGAGTTATACCCACATCAACTATAAAGTCAGCATGGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575677.3 3/1
ACCTGGAGCAGACCGTGACCAGGCTGACTCGTGGGGAACTGAGTGCTGAGGAAGTGACCCTGGTCTGTGAGAAGGTGCTGGATGAAGCAGATGGAGACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575677.4 4/1
CTTCTCAGCCACCCATGAACTGTACAGTATACAGTCTTCTCGGTCTTCAGACAGACTGGAACTTGGAATGAATTTGTTGTGCTGCATACCTGGCAGATTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575677.5 5/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575677_2.fastq <==
@SRR6575677.1 1/2
NAGCTAAGGAATTCTCCAAGACATGGATGTACTCGACAAAAACTCTCATGCTGCCATGTTCTTCTATCTTTTCTATTTTGTCAGTGGCCAGCATAATAGT
+
#-F---FFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFF-FFFFFFFFFFF-FFFFFFF--FFFFFFFF-FFF--F-FF-FFFFF--F-FF-F8FF--F
@SRR6575677.2 2/2
NGCCTGTGTTCTCTCAGAGTCGTCTTCTGGGCATACTCTGAGCTGCTTTGCTGGGAAAGACTTTTGTGTAAAGAAGGGATTAGAGGGAGTATATGAGGAA
+
#--FFFFFFFFFFFF-F-FFFFFF-FFFFFFF-F-FFF-F---FF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF8FFFFFFFFF--FFFF8FFFF
@SRR6575677.3 3/2
NCAGAGTAGAGATGGGTGAGGGCCAGGTCTTGTCCTCTGAGCATGTCAGATGCGGATGTGGAATGTGCTGAGGAAGTCTGGAGCTCGCAGGATCATATTT
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF--F-FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF
@SRR6575677.4 4/2
NGTTTTCTACTACCTGGTCATGGCCCAGGGAAGCATCATCCAGACTGGAAACCATACTCACCAGGTGGAGCCAGGAGAAGCTCCAGTAAAAGGCAACTTT
+
#FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFF-FFFF-FFFFFF-FFFF-FFFFFFFFFFFFFFFFF-FFFF-FFFF-F-FFF
@SRR6575677.5 5/2
NCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGG
+
#FFFF-FFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-F-FF-FFFFFFFFFFFFFFFFFFFF-FFFFFFF

Starting FASTQC command


Processing SRR6575677_1.fastq

Printing command:
fastqc --outdir SRR6575677_1.fastq

Analysis complete for SRR6575677_1.fastq

Processing SRR6575677_2.fastq

Printing command:
fastqc --outdir SRR6575677_2.fastq

Analysis complete for SRR6575677_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.4G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 G4-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 678M Oct 12 19:41 SRR6575677_1.fastq
-rw-r--r--   1 kkarri waxmanlab 678M Oct 12 19:41 SRR6575677_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:09 EDT 2018
0 hours, 1 minutes and 41 seconds elapsed.
==========================================================