ERROR: NO COMMON CONTIGS FOUND BETWEEN THE BAM FILE AND THE FASTA FILE

[Axze-rgb]

Hello, sorry this is a duplicate, but I don't know if you see when someone comments on a closed issue: https://github.com/KolmogorovLab/hapdup/issues/18

Also, the solution is not really explicit, "delete the filter bam", I don't understand how to proceed from there. Here is the hapdup.log

[2024-02-24 13:44:51] root: INFO: Filtering alignments
[2024-02-24 13:48:23] root: INFO: Running: flye-samtools index -@4 /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/filtered.bam
[2024-02-24 13:48:41] root: INFO: Running: pepper_variant call_variant -b /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/filtered.bam -f /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/assembly.fasta -o /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper -m /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper/pepper_model.bin -t 24 -s Sample --ont_r9_guppy5_sup --include-supplementary --no_quantized 2>&1 |tee /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper/pepper.log
[2024-02-24 13:48:42] root: ERROR: Missing output: /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper/PEPPER_VARIANT_FULL.vcf
[2024-02-24 13:50:37] root: INFO: Filtering alignments
[2024-02-24 13:54:09] root: INFO: Running: flye-samtools index -@4 /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/filtered.bam
[2024-02-24 13:54:28] root: INFO: Running: pepper_variant call_variant -b /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/filtered.bam -f /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/assembly.fasta -o /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper -m /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper/pepper_model.bin -t 24 -s Sample --ont_r9_guppy5_sup --include-supplementary --no_quantized 2>&1 |tee /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper/pepper.log
[2024-02-24 13:54:28] root: ERROR: Missing output: /media/alessandro/Storage/MA/P2/SNP_analysis/H5A2_Flye_assembly/hapdup/pepper/PEPPER_VARIANT_FULL.vcf

Thanks a lot

EDIT: what drives me crazy is that it works perfectly with all my other samples, only in this one it seems to use the filtered bam to get the contig names

[Axze-rgb]

Ok, I remade the bam file (the original one, not the filtered one) out of desperation, and relaunched HapDup via Singularity. It crashed the same. I then redid a mapping (a second time) and launched again because why not? I have nothing better to do (I hate my life). It's still running but way beyond the point of the error for which I opened this thread. I have no idea of what happened. I keep this open in case you have an explanation; so far, I am inclined to believe my computer has developed sentience and is trolling me.

[mikolmogorov]

Hello,

I think PEPPER for some reason did not produce any output. Could you send the corresponding log file? And what is the genome you are trying to assmeble?

[Axze-rgb]

Hello, Irelaunched the initial mapping and everything and it worked. It's a non model species with high heterozygosity so we are investigating if HapDup can actually handle something like 3% heterozygosity. My understanding is it relies on tools trained on humans so there is a chance we encounter problems. Thanks

[mikolmogorov]

Ok, glad it worked! 3% heterozygosity is indeed 30x higher than human heterozygosity.. This may be a challenge for Hapdup. I expect that initial haploid assembly will have a mix of haploid and diploid contigs. I would try deduplicating the initial assembly with purge_haplotigs before applying Hapdup.

[Axze-rgb]

I will try that, do you have tools to evaluate the phasing quality? Any recommendations? Thanks.

[mikolmogorov]

The best method would be using trio or Hi-C, anything that can give you orthogonal info about phasing.