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Rosella recover flight status error #30
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Hmm, yeah that error is not very informative. Would you please provide the reference file and coverage file? I'll see if I can get to the bottom of it Rhys |
Files are attached, thanks! |
Hi! So i've looked through your files and tried running Rosella on them. You are right that rosella does error out, but I believe it is not due to a problem on rosella's end. The assembly you are trying to bin is not very good, here are the stats from bbmap for it:
As you can see, most of the contigs fall below the default minimum contig size that rosella uses ( I think I will go ahead and close this issue now. Hopefully you have found my response helpful, and you can find something useful in your assembly. Cheers, |
Hello Rhys, Thanks again for building rosella and the great support! |
You can certainly try it out, you just have to set You'll probably also want to alter |
This was certainly helpful, thanks! |
Hi, I have tried a few things, contig size and bin size were lowered. Unfortunately, after successfully completing the "Contigs kmers analyzed" part it crashes: [00:07:56] ⠋ Calculating UMAP embeddings and clustering... 3/6 Not sure what that could mean... |
Would you please be able to post the output of |
Hi, thanks for looking into this! packages in environment at /home/jan/.conda/envs/rosella:Name Version Build Channel_libgcc_mutex 0.1 conda_forge conda-forge |
Hi, I am running into an error when running rosella recover with several metagenomes. The error is not consistent between samples, e.g. I cannot predict when the error will occur, however it does happen consistently on the samples with which it occurs. The error statement is:
Error when running flight process. Exitstatus was : ExitStatus(unix_wait_status(256)) thread 'main' panicked at 'Failed to grab stderr from failed flight process', /home/conda/.cargo/registry/src/github.com-1ecc6299db9ec823/bird_tool_utils-0.3.0/src/command.rs:17:14
The original command was:
rosella recover -i S04_1a9817_spa_t_mtb_cov.txt -r S04_1a9817_spa_t_contigs.fa
I can provide the original files if needed, the coverage file was generated by use of coverm contig in metabat mode.
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