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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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stderr throw away (2>/dev/null) during polishing steps results in troubleshooting difficulties #37

Open Sam-Koehler opened 11 months ago

Sam-Koehler commented 11 months ago

Hello,

I was encountering an error during the flye --polish-target step where the files flye_hap_1/polished_1.fasta and flye_hap_2/polished_2.fasta were not being generated. I was eventually able to determine that my issue was not related to the HapDup software itself, but from my own operating system (OSError: AF_UNIX path too long) which I then resolved by reducing the length of my output directory path. Currently, HapDup throws away the stderr log during this polishing step that would have helped me identify my issue sooner. Is there a reason that this stream is not logged?

Thanks for the support, I'm really enjoying your tool!

Sam

mikolmogorov commented 11 months ago

Thanks for your report! Good idea, I will preserve stderr output in the next versions.