.maf file not produced ?

hsinnan75 / GSAlign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

MIT License

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.maf file not produced ? #12

Closed Manisha0328 closed 3 years ago

Manisha0328 commented 3 years ago

Hello, First of all, thanks for this amazing fast genome alignment tool!

The program does not output .maf file for an alignment between two .fasta files. However, all other files are produced after alignment is done. Attached screenshot shows some of the last lines of console output.

Please help or comment if there is some mistake in using the tool efficiently. I really need the .maf file. Many thanks in advance!

Command used: .../GSAlign -t 4 -slen 20 -alen 2000 -i -q -o -fmt 1 -dp

hsinnan75 commented 3 years ago

Hi! It looks like GSAlign could not find alignments between the two sequences. You may use different parameters to lower the thresholds and try again. Since your sequences are not very long, I'll suggest to use -slen 15 -alen 100 or -sen (sensitive mode). If there should be alignments and GSAlign could not detect them, please let me know. Thank you!