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blachlylab / fade

Fragmentase Artifact Detection and Elimination
MIT License
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Exception when adding the bam tag. #22

Closed yangyxt closed 2 years ago

yangyxt commented 2 years ago

I run into this error when simpy trying to run fade annotate. Here is the error log as a screenshot: image

I use GATK ValidateSamFile to check the integrity of BAM file before using them on FADE. So I'm pretty confident my BAM file is not corrupted.

charlesgregory commented 2 years ago

Yes I agree, this doesn't sound like an issue with your bam file. I think I have run into this issue before on a prior version of fade.

Could you try our new 0.5.1 version? It think it should solve this issue. I have uploaded a x86_64 static linux binary to the release.

charlesgregory commented 2 years ago

Continuing from https://github.com/blachlylab/fade/issues/21#issuecomment-1002956965.

I did observe this behavior, though it should be corrected. I can no longer recreate this error with the new 0.5.2 binary and my test data. Would it be possible for you to provide a sample of your bam file that produces the issue so I can reproduce it and perform testing?

charlesgregory commented 2 years ago

Actually that may not be necessary yet. I have managed to recreate the error. I will investigate the source of the error.

charlesgregory commented 2 years ago

@yangyxt, I have now added another release, v0.5.3. I specifically was able to recreate the issue you observed and create a solution. I have also fixed another crash that was occurring randomly. Could you please try the 0.5.3 release? I appreciate and thank you for your patience through this process.

You may see this appear in the log from fade v0.5.3:

[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...

This message just indicates that the bug was hit and we are running the work-around for it, but it is not an error.

yangyxt commented 2 years ago

@yangyxt, I have now added another release, v0.5.3. I specifically was able to recreate the issue you observed and create a solution. I have also fixed another crash that was occurring randomly. Could you please try the 0.5.3 release? I appreciate and thank you for your patience through this process.

You may see this appear in the log from fade v0.5.3:

[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...

This message just indicates that the bug was hit and we are running the work-around for it, but it is not an error.

Thank you for the improvement. I'll try it now.

yangyxt commented 2 years ago

@yangyxt, I have now added another release, v0.5.3. I specifically was able to recreate the issue you observed and create a solution. I have also fixed another crash that was occurring randomly. Could you please try the 0.5.3 release? I appreciate and thank you for your patience through this process.

You may see this appear in the log from fade v0.5.3:

[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...

This message just indicates that the bug was hit and we are running the work-around for it, but it is not an error.

I just tried and it seems worked. The logging info are pasted below: image

charlesgregory commented 2 years ago

Yep looks good. I will close this now. If you see anymore errors or have any issues, please open an issue. Thank you for helping us find this and for using fade!