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This will show something like:
| Code Block |
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------------------------------------------------------------------ ..Done alignmentUtils.pl bamstats - 20202022-06-1410 2312:1959:3805 .. samstats file 'bwa_global.samstats.txt' exists and is not empty - 20202022-06-1410 2312:1959:3805 =============================================================================== ## Cleaning up files (keep 0) - 20202022-06-1410 2312:1959:3805 =============================================================================== ckRes 0 cleanup =============================================================================== ## All bwa alignment tasks completed successfully! - 20202022-06-1410 2312:1959:3806 =============================================================================== |
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The great thing about pipeline scripts like this is that you can perform alignments on many datasets in parallel at TACC, and they are written to take advantage of having multiple cores on TACC nodes where possible.
On the stampede2, with its 68 physical cores per node, they the ls6 the pipeline scripts are designed to run best with no more than 4 tasks per node. Although each ls6 node has 128 physical cores per node, the alignment workflow is heavily I/O bound overall, and we don't want to overload the file system.
| Tip | ||
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These alignment scripts should always be run with a wayness of 4 (-w 4) in the stampede2 ls6 batch system, meaning at most 4 commands per node. |
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- Navigate to http://www.ncbi.nlm.nih.gov/nuccore/NC_012582
- click on the Send to down arrow (top right of page)
- select Complete Record
- select File as Destination, and Format FASTA
- click Create File
- in the Opening File dialog, select Save File then OK
- Save the file on your local computer as NC_012582.fa
- click on the Send to down arrow (top right of page)
- Back on the main http://www.ncbi.nlm.nih.gov/nuccore/NC_012582 page
- click on the Send to down arrow (top right of page)
- select Complete Record
- select File as Destination, and Format GFF3
- click Create File
- in the Opening File dialog, select Save File then OK
- Save the file on your local computer as NC_012582.gff3
- click on the Send to down arrow (top right of page)
- Repeat steps 1 and 2 for the 2nd chromosome
- NCBI URL is http://www.ncbi.nlm.nih.gov/nuccore/NC_012583
- use NC_012583 as the filename prefix for the files you save
- you should now have 4 files:
- NC_012582.fa, NC_012582.gff3
- NC_012583.fa, NC_012583.gff3
- Transfer the files from your local computer to TACC
- to the ~/scratch/core_ngs/references/vibCho directory created above
- On a Mac or Windows with a WSL shell10 or later, use scp from your laptop
- On Otherwise on Windows, use the pscp.exe PuTTy tool
- See Copying files between TACC and your laptop
- On a Mac or Windows with a WSL shell10 or later, use scp from your laptop
- to the ~/scratch/core_ngs/references/vibCho directory created above
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