MiGMAP long run time

Could anyone advise on average runtime for the MiGMAP tool to map BCR sequences from single cell data? I started a MiGMAP run with a collection of 37 paired reads from a single cell sequencing experiment (SmartSeq, Nextera, HiSeq4000) 3.5 weeks ago and it is still showing in orange and as ‘currently running’. Does this tool just take a long time or is it likely there is an error?

And are there any alternative tools in Galaxy to extract BCR variable region sequences from single cell data?

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Hi @carolyn_nielsen

Would you confirm that you are working at usegalaxy.eu. If somewhere else, please note the server URL. Thanks!

cc @gallardoalba

Working at humancellatlas.usegalaxy.eu. Thanks.

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Hi @carolyn_nielsen,
we have increased the number of cores assigned to this tool. Please repeat the analysis in a few hours.

Regards

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Great thank you will try that.

@carolyn_nielsen the job is still running. But slowly. I see logging message in the last minutes like

[Mon May 17 12:47:55 CEST 2021 MIGMAP +4159m15s] Loaded 1690 reads. Processed 871 reads, of them 85.76% mapped. Among mapped reads 97.45% passed quality filter and 0.0% passed all filters.

Its doing something, but no clue how long this will take.
We have granted more compute resources to this tool (now 12 CPUs), so you could try to restart one job and see if its faster.

Hope that heps,
Bjoern

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Thanks Bjoern - I restarted on Tuesday so hopefully will be a bit faster.

Lets see. The tools sees to be mostly sleeping. Not much we can do here, its seems to be inefficient :frowning:

Still running! Are there any plans to make any other BCR tools available on Galaxy? e.g. BALDR or BraCeR?

@carolyn_nielsen I have no clue. This tool seems to be super slow. The multiple cores are not to be utilized much :frowning:

Do you have recommendations about BALDR and Bracer? wth which one we should start if we would have time?

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@carolyn_nielsen there is really something wrong. Can you please subsample your input file to a tiny tiny file or if you know some small files where you know those are working us them to see if you get some results. I suspect there is something wrong with your input data.

I also see this in the logs, for weeks … :frowning:

[Thu Jun 10 09:16:06 CEST 2021 MIGMAP +19065m32s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:16:16 CEST 2021 MIGMAP +19065m42s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:16:26 CEST 2021 MIGMAP +19065m52s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:16:36 CEST 2021 MIGMAP +19066m02s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:16:46 CEST 2021 MIGMAP +19066m12s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:16:56 CEST 2021 MIGMAP +19066m22s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:17:06 CEST 2021 MIGMAP +19066m32s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:17:16 CEST 2021 MIGMAP +19066m42s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:17:26 CEST 2021 MIGMAP +19066m52s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:17:36 CEST 2021 MIGMAP +19067m03s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:17:46 CEST 2021 MIGMAP +19067m13s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:17:56 CEST 2021 MIGMAP +19067m23s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:18:06 CEST 2021 MIGMAP +19067m33s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:18:16 CEST 2021 MIGMAP +19067m43s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:18:26 CEST 2021 MIGMAP +19067m53s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:18:36 CEST 2021 MIGMAP +19068m03s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:18:46 CEST 2021 MIGMAP +19068m13s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:18:56 CEST 2021 MIGMAP +19068m23s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:19:06 CEST 2021 MIGMAP +19068m33s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:19:16 CEST 2021 MIGMAP +19068m43s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:19:26 CEST 2021 MIGMAP +19068m53s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:19:36 CEST 2021 MIGMAP +19069m03s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:19:46 CEST 2021 MIGMAP +19069m13s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:19:56 CEST 2021 MIGMAP +19069m23s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:20:06 CEST 2021 MIGMAP +19069m33s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:20:16 CEST 2021 MIGMAP +19069m43s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:20:26 CEST 2021 MIGMAP +19069m53s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:20:36 CEST 2021 MIGMAP +19070m03s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:20:46 CEST 2021 MIGMAP +19070m13s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:20:56 CEST 2021 MIGMAP +19070m23s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.
[Thu Jun 10 09:21:06 CEST 2021 MIGMAP +19070m33s] Loaded 15625 reads. Processed 6027 reads, of them 89.28% mapped. Among mapped reads 97.9% passed quality filter and 0.0% passed all filters.

Thanks for this! I am just confirming with collaborator which is recommends. Believe there is also another option called MiXCR.

Ok yes don’t think MiGMAP will work- just returned errors on the original submitted samples:

Will get back to re alternative tool.

HI @bjoern.gruening - would be great if a MixCR wrapper could be added to Galaxy: MiXCR: a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data — mixcr documentation

Let me know if you think this might be feasible!

Hi @bjoern.gruening any thoughts on this? Installation — mixcr documentation

Hi @carolyn_nielsen,
I created an issue about it: Request for tool MiXCR.

Regards

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Hi @carolyn_nielsen,
this tool is already in Galaxy: MiXCR.

Regards

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Ah thank you @gallardoalba I had just looked on the Human Cell Atlas instance!

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