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blachlylab / fade

Fragmentase Artifact Detection and Elimination
MIT License
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Warning or error log in fade annotate ? #31

Closed xiucz closed 2 years ago

xiucz commented 2 years ago

Hi, Thanks for your tool, when I test it for my panel data, it shows following log, should I ignore it?

Version: fade.many-linux-x86_64.tar.gz

fade annotate -t 8 -b $filein $ref_hsa > test.fadeanno.1.bam

Here is the log on screen:

[W::fade annotate] Output SAM/BAM will not be sorted (regardless of prior sorting)
[I::dhtslib.sam.reader.SAMReader.__ctor!string.this] 6 CPU cores detected; enabling multithreading
[I::dhtslib.sam.writer.SAMWriter.__ctor!(File).this] 6 CPU cores detected; enabling multithreading
[W::dparasail.alignment.Parasail.this] Couldn't load matrix named ACTGN, assuming alphabet
[W::dparasail.alignment.Parasail.this] Attempting to create matrix from alphabet ACTGN
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...
[I::dhtslib.sam.record.SAMRecord.opIndexAssign!ubyte.opIndexAssign] Undefined issue adding/updating bam tag. Trying again...

Best, xiucz

charlesgregory commented 2 years ago

This is an issue that occurs rarely when fade is modifying the bam tags on a bam file. The message you see is just an indicator that the error occurred and it tries again to modify the tag. The issue in full is discussed over on dhtslib in issue https://github.com/blachlylab/dhtslib/issues/127. I am not sure if the true problem resides in fade, dhtslib or htslib as it is difficult to re-create outside of the setting of running fade.

The message is just a indicator for future debugging.

xiucz commented 2 years ago

@charlesgregory Thank you , I will close this issue.