-----------------------
Start of variable list:
-----------------------
Sample_ID:
B4-MAA100140-3_57_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 19:42:20 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790982
Current job name : Step_02_B4-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790982.1.linga

Loading required modules...


List files in scratch directory:

total 92M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 B4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  46M Oct 12 19:42 SRR6575968_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  47M Oct 12 19:42 SRR6575968_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575968_1.fastq <==
@SRR6575968.1 1/1
CCTAAAACAGAAGGTAGCCCAGCTTGAAGCCCAGTGCCAGGAGCCTTGCAAGGACTCTGTGCAAATCCATGACACAACTGGAAAAGATTGTCAGGAAATT
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575968.2 2/1
GATAATAGGAGCAGTACGGCTGTAATAAGTACGGATCAGACAAATAGTGGAGTTTGATACTGTGTTATGGCTGGGGGTTTCATGTTGATAATAGTGGTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575968.3 3/1
GAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTACAAAACCATCATAAATTTAAATACAAACCAAATTAAATTACACCCAGATGATAATGGTGTAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF888-F8----------FF-F----FF---FF-F--F--FFF-FFF------F------FF---
@SRR6575968.4 4/1
GCTGAGGAAGGGGAGTCAAGTAAGCAATGGTGTGGTAGATCCGAGCACCTACAAAGATTCTGAAGTGCATGAGGGCTGTAGAGAGATCTGGTCCACTCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575968.5 5/1
ACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCC
+
FFFFFFFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF

==> SRR6575968_2.fastq <==
@SRR6575968.1 1/2
NATCCTGTTCCGCACAGTTGCCTTCAAACTTATCGTTGTCGTTGTCCCAGGTACTGAACTGCATGCCGTTGTGGGATGTGAAAAACTTGTCACTGGGGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F--FFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFF-FFFFFFFFF-FFF8FFFF-FFFFF-FF8F
@SRR6575968.2 2/2
NGCCCATGCAGGAGCATCAGTAGACCTAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTATTTTAGGTGCAATTAATTTTATTACCACTATTATC
+
#FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFF8FFFF
@SRR6575968.3 3/2
NTCCAGTGATGGGACCGGGCAGAGCCCCTATTTCCTTAGAGAACTCTGAATCCAGATAAGGAACTGAGCCATCCACACGATGAAGGAGGGCTTCTAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF
@SRR6575968.4 4/2
NTGCCAACCCAGAAGACTACGCTGGCTTTGGCAAGGGAGGGAATGCCAAGAAGTTTGTTCGCACTGACGAGAAGGTGGAACGCGTGCGCAGAGCCCACCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575968.5 5/2
GCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGAT
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFF

Starting FASTQC command


Processing SRR6575968_1.fastq

Printing command:
fastqc --outdir SRR6575968_1.fastq

Analysis complete for SRR6575968_1.fastq

Processing SRR6575968_2.fastq

Printing command:
fastqc --outdir SRR6575968_2.fastq

Analysis complete for SRR6575968_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 494M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 B4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 247M Oct 12 19:42 SRR6575968_1.fastq
-rw-r--r--    1 kkarri waxmanlab 247M Oct 12 19:42 SRR6575968_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:07 EDT 2018
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================