jnarayan81/parallellastz

parallelLastz: Running Lastz in parallel

parallelLastz

Lastz with multi-threads support.

Running Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors.

When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original lastz program. This is useful when you lastz a big query file to a huge reference like human whole genome sequence.

The program is an extension on the original lastz program which was written by Bob Harris (the LASTZ guy).

parallelLastz can run on Linux and Mac OS.

It run lastz in parallel mode and generate .lz (tab file) file.

perl parallelLastz.pl -h for more help

--qfile|-q	query multifasta/fasta file
--tfile|-t	target genome file
--cfile|-c	config file
--speedup|-s	number of core to use
--length|-l	length below this is ignored
--help|-h	brief help message

Conda

To install parallelLastz conda packages, in the terminal or an Anaconda Prompt, run:

conda install -c jnarayan81 parallellastz

The test data can be found at https://github.com/jnarayan81/parallelLastz/tree/master/testDATA, and the sample configuration file at https://github.com/jnarayan81/parallelLastz/blob/master/conf.

Citation

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University.

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Help

Contact me at [email protected] or [email protected]

parallellastz's Issues

parallelLastz.pl finds a local lastz binary but exits anyway?

Is line 53 in parallelLastz.pl correct?

That appears to kill the program regardless of whether it finds a local lastz binary. Sure enough, when we ran it locally on our machine it reports that it finds the local lastz binary and then prints that error and kills the process.

Commenting that entire line out allowed us to run the program properly, so there seems to be an issue with the check.

Target Query mixed up

Hi Jitendra. Thank for making available the script. I ran it over the last few day, and it seems that the target (--tfile) and query (--qfile) have been mixed up - the results aligned the target to the query. Is it possible to have a look at your code and see where it has gone wrong - I have not been available to work it out. Hope you can help. A

getting the same message as --help every time

Hello,

I keep getting this message every time I try to run this:

                   _ _      _   __           _

_ __ __ _ _ __ __ | | | | | / / __ _ | | ____
| ' \ / | '__/ _ | | |/ _ \ |/ / / ` / __| _| /
| |) | (| | | | (| | | | / / /| (| _ \ | / /
| .__/ _,|| _,|||_|_/_,|/_/|v0.1
||
parallelLastz: Run lastz jobs in parallel
Contact: [email protected] for support

parallelLastz 0.1

Usage: /work/GGA_circos/maskedgenome/parallelLastz/parallelLastz.pl --qfile <> --tfile <> --cfile <> --speedup <#>

Options:
--qfile|-q query multifasta/fasta file
--tfile|-t target genome file
--cfile|-c config file
--speedup|-s number of core to use
--length|-l length below this is ignored
--unmask|-u unmask the lowercase in t and q file
--wipe|-w wipe out the intermediate files
--help|-h brief help message

The command I am using is:

perl /work/GGA_circos/maskedgenome/parallelLastz/parallelLastz.pl -q /work/GGA_circos/maskedgenome/parallelLastz/testDATA/qsample1.fa -t /work/GGA_circos/maskedgenome/parallelLastz/testDATA/tsample.fa -c /work/GGA_circos/maskedgenome/parallelLastz/conf --speedup 36

I am not sure what is wrong.

Any help is greatly appreciated.

Best,
Basanta

getting the same --help message as every time

the output is just the --help message