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?
Would you confirm that you are working at usegalaxy.eu. If somewhere else, please note the server URL. Thanks!
Hi @carolyn_nielsen,
we have increased the number of cores assigned to this tool. Please repeat the analysis in a few hours.
Regards
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
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 
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
Do you have recommendations about BALDR and Bracer? wth which one we should start if we would have time?
@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 …
[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 Gallardoalba,
I’m having trouble with the Galaxy implementation of MiXCR. I talked to the lab that created MiXCR, and they feel that it is an issue with the Galaxy side of things.
I’m having trouble viewing the 512 successfully aligned TCR clonotypes from MiXCR. See 1) report of successful MiXCR run with 513 clonotypes and 2) empty clonotype file
Analysis date: Thu Oct 28 16:38:14 CEST 2021
Input file(s): mixcr_analysis.clna
Output file(s): mixcr_analysis.contigs.clns
Version: 3.0.5; built=Mon Feb 25 00:04:20 CET 2019; rev=af538f7; lib=repseqio.v1.5
Command line arguments: --report mixcr_analysis.report mixcr_analysis.clna mixcr_analysis.contigs.clns
Analysis time: 59.16s
Initial clonotype count: 513
Final clonotype count: 513 (100%)
Longest contig length: 553
Clustered variants: 0 (0%)
Reads in clustered variants: 0.0 (0%)
Reads in divided (newly created) clones: 0.0 (0%)
