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MrOlm / inStrain

Bioinformatics program inStrain
MIT License
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DEBUG:no_length will not be considered as part of the genime #163

Closed Xiaoxin9115 closed 1 week ago

Xiaoxin9115 commented 1 year ago

During our inStrain compare process, we encountered a DEBUG message indicating that "no_length will not be considered as part of the genome." However, the length information is displayed in the STB file. We want to know what is the reason for this. Whether effect our result of compare? image image

MrOlm commented 1 year ago

Hi @Xiaoxin9115 - Could you provide the log file from the run?

Thanks, Matt

Xiaoxin9115 commented 1 year ago

log.log

MrOlm commented 1 year ago

OK- what this error means is that that scaffold is not present in the IS file (so was not originally provided during the inStrain profile run). So the line:

23-10-30 20:26:38 DEBUG FAILURE StbError CowSGB-1_c1 CowSGB-1.fa no_length will not be considered as part of the genome

is saying that your stb file says scaffold CowSGB-1_c1 should be in genome CowSGB-1.fa, but the scaffold CowSGB-1_c1 wasn't provided in the .fasta file that was used to make the inStrain profile objects

-Matt