Unable to Run Lumpy

1

When trying to run Lumpy, it is not recognizing that I have the correct input in my directory despite having run Lumpy pre-processing with three outputs (split-read alignments, discordant read pairs, and collated and groomed data). Is there a certain way to correct this or advice for running Lumpy?

2

Dear @shelbigill,
Have you ran Lumpy on a local Galaxy instance or have you used a pblic instance such as usegalaxy.org?

I tested the tool quickly on usegalaxy.eu with some test data and it worked. So if your input is not recognized and you are operating on a public instance, then make sure that your input data for Lumpy pre-processing has not a weird name. You can also check again if all result files are in bam or in a qname_sorted.bam format.

I hope I could help and best wishes,
Florian

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3

Hi Florian,

I was able to input the three required input files after some adjustment, but I’m now presented with an error where it is unable to retrieve the index files for the BAM files input. I know that I have the index files present. How would you recommend handling this?

Thanks,
Shelbi

5

Dear @shelbigill,
Can you check if one of the three input files is empty (i.e., it contains maybe all header lines but the bam file does not contain any reads)?

Cheers,
Florian

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7

Hi Florian,

The three input files all appear to have their data. Nothing is empty. They are being run in collection data sets.

Thanks,
Shelbi

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8

Hi @shelbigill,
the error may be due to the BAM files not having read groups. You can confirm that by visualizing the header of the BAM file. If it doesn’t contain read groups, you can add them it by using AddOrReplaceReadGroups.

Regards

9

Hi @gallardoalba,

I reran the three collections to ensure they had the read groups via AddOrReplaceReadGroups. When inputting into Lumpy, I am still presented with the error that it could not retrieve the bam index file. I have tried running this multiple times with a focus on ensuring the read groups were present before replying.

-shelbigill

1 Like
10

Hello, can anyone help me?
Im having some issues with LUMPY preprocessing too:

I have a WGS sample. i aligned with BWA-MEM and my outputs seems to be ok.
But when i use LUMPY_preprocessing to extracts discordant read pairs and split-read its no working due to: file does not contain alignment data

Does anybody has already used this LUMPY tool?
Is there any BWA-MEM parameter to set before lumpy_preprocessing??

Thanks in advance