Question: mpileup warning and problem with bcftools call
0
gravatar for aymeric.goyer
28 days ago by
aymeric.goyer0 wrote:

I am using mpileup and bcftools call in Galaxy. Mpileup produces a VCF output file, but also gives me the following message.

[warning] tag DPR functional, but deprecated. Please switch to AD in future. [warning] tag DV functional, but deprecated. Please switch to AD in future. [warning] tag DP4 functional, but deprecated. Please switch to ADF and ADR in future.

Then, when I run bcftools call on the mpileup output VCF file, I get the following message:

error An error occurred with this dataset: Fatal error: Exit code 255 () [E::hts_hopen] fail to open file 'input.vcf.gz' [E::hts_open_format] fail to open file 'input.vcf.gz' index: failed to open "input.vcf.gz"

Do you know whether these issues are related and how to fix it?

Thanks

samtools • 92 views
ADD COMMENTlink modified 28 days ago by Jennifer Hillman Jackson25k • written 28 days ago by aymeric.goyer0
0
gravatar for Jennifer Hillman Jackson
28 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

I see successful runs of this tool and a couple of failed runs where the input wasn't a Mpileup result dataset, but instead, the results from a prior BCFtools call job. This would be expected to fail (wrong data content/datatype).

All of the associated datasets are now permanently deleted (purged). Perhaps you discovered the input mixup already?

Troubleshooting FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 28 days ago by Jennifer Hillman Jackson25k

Hello,

Bcftools call was run on the only output file produced by mpileup, so it is not clear to me why bcftools call yielded this error message.

I copied the job information below.

Thanks

Job Information

(admin redacted to preserve data privacy)

ADD REPLYlink written 28 days ago by aymeric.goyer0

In the history named "Sur38" at Galaxy Main https://usegalaxy.org:

  • the bcftools call job (data 31) with input data 30 (Mpileup output) was successful.

  • the bcftools call job (data 34) with input data 31 (bcftools call output) failed.

The Job Details page per dataset can be reviewed to see what was actually executed for any successful or failed jobs (look further down the page, the information you provided is near the top).

If these are not the jobs are you referring too, please send in a bug report from one of the failed datasets (click on the green bug icon in the expanded dataset). It is important that the input and output datasets are left undeleted for full review. Also, please include a link to this post in the comments.

There are three histories associated with your account and all are active: two contain data, one does not. Only the history "Sur38" contains a failed bcftools job and all inputs/outputs associated with these jobs are permanently deleted. You will need to rerun to reproduce and report the error -- unless the above clears this up.

If you are using more than one account at Galaxy Main, we can guide in consolidating your data into a single account and proactively delete the other(s) before they are picked up by the automated duplicate account process (and all removed without notice, often resulting in data loss). Only one account per user is permitted at this and most other public Galaxy servers. This is agreed upon usage when creating an account and also under Help > Terms and Conditions. https://usegalaxy.org/static/terms.html

ADD REPLYlink modified 28 days ago • written 28 days ago by Jennifer Hillman Jackson25k
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