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JiaoLaboratory / CRAQ

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
https://doi.org/10.1038/s41467-023-42336-w
MIT License
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Unknown errors #24

Open xiadawei123 opened 1 month ago

xiadawei123 commented 1 month ago

Hi, thanks to the development of this tool, I used short reads and HiFi reads to evaluate the genome at the same time, and although I got the final result, there seems to be some errors in the log file related to the alignment, and now I'm not sure if I really ran it successfully. Looking forward to your reply craq.log out_final.Report.txt

JiaoLaboratory commented 4 weeks ago

it seems some errors in craq running. by the way, could you check is the Output/LRout/LR_sort.bam and LR_sort.depth normally generated or is empty? if not, maybe CRAQ run disturbed by someing (maybe the CPU memory). If the LR_sort.bam is normal, you cound rerun CRAQ by running " ln -s Output/LRout/LR_sort.bam ./ && ln -s Output/SRout/SR_sort.bam && craq -g Your_assembly.fa -sms LR_sort.bam -ngs SR_sort.bam " .
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