search

bioinf / Sibelia

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.
http://bioinf.spbau.ru/sibelia
Other
64 stars 17 forks source link

C-Sibelia.py does not create VCF file #176

Closed Rhinogradentia closed 6 years ago

Rhinogradentia commented 7 years ago

Hi,

I'm trying to call Variants using C-Sibelia.py. I've managed to do it with other sequences (very similar) before, but now I am stuck with a sequence combination where no VCF file is created (no maf and no unmapped file as well). What could be the reason for this? How can I fix this? I've already tried the loose option and changed the block size, but neither of this changed something.

The call I am using looks like this:

C-Sibelia.py -o outdir/ --maf seq1_vs_seq2.maf -v seq1_vs_seq2.vcf -u seq1_vs_seq2.txt seq1.fa seq2.fasta

In contrary to other runs all the tmp-files are still there (block.anchors, block.fasta, blocks_coords*.txt)

Thank you for your help

Best Regards,

Nadine

iminkin commented 7 years ago

Hi Nadine,

It looks like the alignment got interrupted. It could be due to a bug in the aligner we use (LAGAN), or some problems with Sibelia. Can you share .fasta files? Or at least blocks_coords.txt?

Rhinogradentia commented 7 years ago

Hey there,

I can provide the blocks_coords.txt. It's attached.

blocks_coords3.txt blocks_coords2.txt blocks_coords1.txt blocks_coords0.txt

Thank you,

iminkin commented 7 years ago

You may try to change the parameter -m slightly. If it is a problem with the aligner, maybe slightly changed output will get rid of "bad" data.

Rhinogradentia commented 6 years ago

Thank you, sorry for the late answer. I've tried that now with several values. Below -m 500 I get the same result. From -m 1500 on I get following Error: An error occured: [Errno 2] No such file or directory: 'Seq1_vs_Seq2.vcf'. The resulting files are the blocks_coord txt files, blocks_sequences.fasta, coverage_report.txt, d3_blocks_diagram.html, genomes_permuations.txt and the circos folder. I've also tried to create the file beforehand with touch. This changed nothing in the outcome.

Do you have any further idea?

Best Regards,

Rhinogradentia commented 6 years ago

Managed to produce a valid vcf file now with -m 800 and a shorter out-dir-path. Maybe the result file would have been to big with -m 1500...

Anyway - thanks for your help.

Best Regards