-----------------------
Start of variable list:
-----------------------
Sample_ID:
P3-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 19:42:18 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790904
Current job name : Step_02_P3-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/8790904.1.linga

Loading required modules...


List files in scratch directory:

total 32M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:42 SRR6576741_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:42 SRR6576741_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576741_1.fastq <==
@SRR6576741.1 1/1
CCTTAGACGCTTCATGATCTAACAACTTACTATGGTTGGCATGCATAATAGCATTTCTTATTAAAATACCATTATATGGAGTTCACCTATGACTACCAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576741.2 2/1
GCATTTGCTGGTCCGGCTATCATTTTTATGCCAATGTCCAGCATGCTAGCAGATGTGCCCAGGGGGAGCATACTCTTGGGGTAGAGGGTGAAGTCCTGAG
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576741.3 3/1
ATGTAAACAATGTGGTAAAGCCTTTTCACAAAGCAGTCATCTCCGAATACATAAGCGAACACATACAGGAGAGAAACCCTATGAATGTAACCAATGTGGA
+
FF8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFF-FFF-FFFFF
@SRR6576741.4 4/1
ACACTCTTCTTCAACGCCTGCTGCCTGGGCTTCGTTGCCTATGCCTACTCTGTGAAGTCTAGGGACAGGAAGATGGTGGGCGATGTGGTTGGAGCCCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576741.5 5/1
ATGTTGGGCAGGGTGGCATAGCGAGGCTCATTGAGCCTTAGGTCAGCAGTCACCACAGCGGGCAGCTTCAGGCGAAGGGTCTCCAGACCCCCGTCAATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576741_2.fastq <==
@SRR6576741.1 1/2
GGGTAGTGCTAGATTAGCTAGACTTGCTATCAGTCATCATGTGGCTATAAGTGGGAAGACCATTTGAAGTCCTCGGGCCAGGATTATAGTACGGCTGTGG
+
FFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFF-FFFFFF8F
@SRR6576741.2 2/2
GATGGAAATCAGAGGAGACCCCCAAAAGGGAAAGTCTCTGATCCGGTAGAGGTCATATCCACCTTCTCCCTGAGCTCTAACAAGCAGTTTCTAATGTCTG
+
F-FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576741.3 3/2
GTATAGAATACTGCAAAGGCTTTACCACATTGTTTACATTCATAGGGTTTGTCTCCTGTATGTCTTCGCTAATGTATGTGGAGATGACTGCTATGTGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FF--8FFFFF
@SRR6576741.4 4/2
GTGGAGCACAGGGCAGCTAGAATCCAGAATGGGGTGTTCTTTGTGCAAAAGACTGAAAGACTACCACAGAGGTGGTAGAGAAAATAATGATGCAGATAAT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576741.5 5/2
CCTAAGCTTTCTGCCTGTGCCCCTGGTATCTCCACGTGGATGCCTCTGTCTGCACCCATGGCCAGAGCAGTTCGGATGGTCTCCTGGCCAAGCTGGCTGA
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576741_1.fastq

Printing command:
fastqc --outdir SRR6576741_1.fastq

Analysis complete for SRR6576741_1.fastq

Processing SRR6576741_2.fastq

Printing command:
fastqc --outdir SRR6576741_2.fastq

Analysis complete for SRR6576741_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 165M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  83M Oct 12 19:42 SRR6576741_1.fastq
-rw-r--r--   1 kkarri waxmanlab  83M Oct 12 19:42 SRR6576741_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:46 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================