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EichlerLab / pav

Phased assembly variant caller
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MissingInputException in native running #54

Open dingyigithub opened 2 months ago

dingyigithub commented 2 months ago

Hi,

When I am trying to run PAV natively with command as 

snakemake -s /storage/yangjianLab/dingyi/tools/pav/Snakefile --cores 2

It threw an error:

image

And when I tried generating an empty file named HG002.vcf.gz, the snakemake ended and displayed:

image

The assemblies.tsv and config.json were both there. I don't know what's wrong with it (x_x) ... By the way, my snakemake is version 8.18.2, Is it a problem with the version？ Extremely thankful for your response！

paudano commented 2 months ago

My apologies for not getting to this sooner. I think the default rule for VCFs isn't working right. I'll fix this in an upcoming version and push it out. Were you able to run PAV?

paudano commented 2 months ago

The change in VCFs leaked through before I intended, I am working on a major release for PAV now. I've fixed this version, and I'm testing now through the default rule. Once the pipeline completes, I'll push v2.4.2.

dingyigithub commented 2 months ago

The change in VCFs leaked through before I intended, I am working on a major release for PAV now. I've fixed this version, and I'm testing now through the default rule. Once the pipeline completes, I'll push v2.4.2.

Hi paudano， Thanks for your reply! I also guessed it is due to the change accidentally uploaded so I used the previous version 2.3.4, and happily it worked. However, just now, when running the last job vcf_write_vcf in snakemake, an error message was displayed: "RuleException: TypeError in line 226 of /storage/yangjianLab/dingyi/tools/pav-2.3.4/rules/vcf.snakefile: header_list() got an unexpected keyword argument 'ref_file_name'." The corresponding code in the vcf.snakefile is like:

image

I'm not sure whether it is an issue with svpoplib or with my data. Thank you again for your help. 🤝

dingyigithub commented 2 months ago

I edit the parameter "ref_file_name" to "ref_filename" and it worked. Maybe it is due to the slight difference between different svpop versions. Thanks very much!

The change in VCFs leaked through before I intended, I am working on a major release for PAV now. I've fixed this version, and I'm testing now through the default rule. Once the pipeline completes, I'll push v2.4.2.

Hi paudano， Thanks for your reply! I also guessed it is due to the change accidentally uploaded so I used the previous version 2.3.4, and happily it worked. However, just now, when running the last job vcf_write_vcf in snakemake, an error message was displayed: "RuleException: TypeError in line 226 of /storage/yangjianLab/dingyi/tools/pav-2.3.4/rules/vcf.snakefile: header_list() got an unexpected keyword argument 'ref_file_name'." The corresponding code in the vcf.snakefile is like:

image

I'm not sure whether it is an issue with svpoplib or with my data. Thank you again for your help. 🤝

paudano commented 2 months ago

I saw that error too, yes, it changed with the last SV-Pop release to harmonize naming conventions. Something got out of sync with PAV (SV-Pop is a submodule). I think I had to delete __pycache__ in dep/svpop/svpoplib on my system before it went away (in a testing native install).

I am temporarily releasing 2.4.1.2. I want to do more testing before I call it a stable release (any PAV version with a fourth number is a development version). It's out now if you want to try it. I expect 2.4.2 this week or next (it's going to be a busy week).

dingyigithub commented 2 months ago

Looking forward to it! Wish you good luck and thanks for kindly help :)