StbError and Could not cluster genomes

[Swt623]

Hello @MrOlm,

I ran inStrain compare for dereplicated MAGs assembled from short-read metagenomic sequences and got the same errors as the first two mentioned in the previous issue. I got StbError for some scaffold-bin with "no_length will not be considered as part of the genome" and "Could not cluster genomes" error. I checked my genomes_fa file and these scaffolds exist.

Checking the output files, I only got genomeWide_compare.tsv and comparisonsTable.tsv, there is no strain_clusters.tsv and the inStrainCompare_dendrograms.pdf file is corrupted.

I attached the log file and the commands I used to run inStrain. Could you help me to check what the problem could be?

Thank you very much!
Weitao

Step3-4_error_messages.txt
log.log
bash_script.txt

[MrOlm]

Hi Weitao,

This issue is coming up because inStrain thinks these scaffolds were not profiled with inStrain profile. For example, it thinks that scaffold "NODE_1_length_51055_cov_4.714171" in genome "002_PWH0091_R_bin.11.strict.fa" was not present in any of the inStrain profile objects.

Can you confirm that the exact same .fasta file and the same .stb file were provided to all inStrain profile runs?

Best,
Matt

[Swt623]

Hi Matt, Thank you for your reply. I am sure I used the same .fasta file and the same .stb file for all inStrain profile runs. Is there any other cause for this issue? Best, Weitao

…

On Jan 1, 2025, at 2:39 PM, Matt Olm ***@***.***> wrote: Hi Weitao, This issue is coming up because inStrain thinks these scaffolds were not profiled with inStrain profile. For example, it thinks that scaffold "NODE_1_length_51055_cov_4.714171" in genome "002_PWH0091_R_bin.11.strict.fa" was not present in any of the inStrain profile objects. Can you confirm that the exact same .fasta file and the same .stb file were provided to all inStrain profile runs? Best, Matt — Reply to this email directly, view it on GitHub <#198 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASRGHJR5QFRRHWWVTN34U6L2IQ77JAVCNFSM6AAAAABTZCK5I2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNRXGEZDGMJVGM>. You are receiving this because you authored the thread.