-----------------------
Start of variable list:
-----------------------
Sample_ID:
A8-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 19:42:19 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790947
Current job name : Step_02_A8-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/8790947.1.linga

Loading required modules...


List files in scratch directory:

total 59M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  29M Oct 12 19:42 SRR6575951_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  30M Oct 12 19:42 SRR6575951_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575951_1.fastq <==
@SRR6575951.1 1/1
TTATAATAAAGAGATTCACAAACCAGGCTATCTGGCTAATGACAGACTCTTACCACAGCGTGTTTTGGAACAACACAAACTGACCAAAGAGCAGTGGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575951.2 2/1
GCTGGCTTCTGATTGGCTGGGGCGAGCAGTGGCCGCAGCAGGCGAAGCCGGTGTTCTCGCACTCGGGTGGCGGCCAGAAACCGGCAGGACTGGAAGGGAC
+
-FFFFFFFFFFFF-FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFF-F
@SRR6575951.3 3/1
CTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGGATTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575951.4 4/1
GCACTGGCGTTGCCCGCGTAATCCATCAGCAGCACCCAGCTGGACAGTATGCTGCAATGGTGCACATCAAGCATGCCCGAGAGCATCATCATGGGCACCT
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFF
@SRR6575951.5 5/1
GTTAAGATCCAGGGTTAGTTTTTGTAGCCTCTGCTGGCCCTTCGGCCTCTGGCGCGCTCAAACTTCCGGCCCTTGGAACGGACATAGGGTTTGGTATGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575951_2.fastq <==
@SRR6575951.1 1/2
GCATCAACACCTAGCCACAGCTCAGTACCCTTCTTATTCTTGATTTCAAAGTAGTTGACACCATACATCTCTAGATCTTGCGCAATCTTCAAGTATTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575951.2 2/2
NTTTATTGTAGATACAAACACGTAACCTCAATATGAGACGTCTAACTAAAGCAAGCACTTCCCATGCCACCAGCTCTTCTAAGGCTTAGGCTTAGGGTTG
+
#-FFFFF-FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFF-FFFFFF-F8FFF8F
@SRR6575951.3 3/2
TGTCAGTATCATGCTGCGGCTTCAAATCCGAAGTGATGTTTTGATGTGAAGTGAAATTTTAGTTGTCGTAGTAGGCAAACAATAAGGAATGTTGATCCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575951.4 4/2
CATGAGATCGCTACAAACCTGGGAGACTTTGCCATCAGCCTATACCGGGAGCTGGTCCATCAGTCCAACACTTCCAACATCTTCTTCTCCCCAGTGAGCA
+
FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575951.5 5/2
GCCGGGGCACTGTGCTCCTGTCTGGTCCTCGGAAGGGCCGAGAGGTGTACCGACATTTTGGCAAGGCCCCAGGAACCCCACACAGCCATACCAAACCCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575951_1.fastq

Printing command:
fastqc --outdir SRR6575951_1.fastq

Analysis complete for SRR6575951_1.fastq

Processing SRR6575951_2.fastq

Printing command:
fastqc --outdir SRR6575951_2.fastq

Analysis complete for SRR6575951_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 324M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 162M Oct 12 19:42 SRR6575951_1.fastq
-rw-r--r--    1 kkarri waxmanlab 162M Oct 12 19:42 SRR6575951_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:54 EDT 2018
0 hours, 0 minutes and 35 seconds elapsed.
==========================================================