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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
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core dumped with ul reads #352

Open hoppo opened 1 year ago

hoppo commented 1 year ago

Hi

I know that the ultra-long read mode is not stable yet, so perhaps the errors I am experiencing is due stability issues. I am using hifiasm-0.17.4 and have tried to incorporate reads greater than >90k I have two hifi fastq files and a single ul file.

Hifiasm processes the data, and it only during the writing of the data that it fails. It has failed in different places, but always during the writing of the data.

...... [M::uidx_write] Index has been written. hifiasm: Correct.cpp:14851: int64_t gen_single_khit(Candidates_list*, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t): Assertion `occ == 0' failed. /job_scripts/9341174: line 25: 695409 Aborted (core dumped)

....... [M::ha_print_ovlp_stat] # reverse overlaps: 17258334 Writing reads to disk... /job_scripts/9341136: line 25: 2599773 Segmentation fault (core dumped)

let me know if you would like any further details

chhylp123 commented 1 year ago

Thanks for reporting this bug. Some other users also reported this issue, but it could be solved by filtering shorter UL reads. I am wondering if is it possible that you can share the UL reads and the bin files with us? I guess this is just caused by a few problematic UL reads.

chhylp123 commented 1 year ago

@hoppo This issue has been fixed in Hifiasm-0.17.6 (r460) beta (see: https://github.com/chhylp123/hifiasm/releases/tag/r460). Could you please have a try? Thanks in advance.

hoppo commented 1 year ago

Hi,

I am testing with the new release - I can let you know if it runs okay. Do you still need the UL reads and the bin files?

Cheers, Marie.

On Sat, 26 Nov 2022 at 03:40, chhylp123 @.***> wrote:

@hoppo https://github.com/hoppo This issue has been fixed in Hifiasm-0.17.6 (r460) beta (see: https://github.com/chhylp123/hifiasm/releases/tag/r460). Could you please have a try? Thanks in advance.

— Reply to this email directly, view it on GitHub https://github.com/chhylp123/hifiasm/issues/352#issuecomment-1327965286, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACIDCCXTRTRXNLUESAIIKM3WKF2DFANCNFSM6AAAAAASLNUYOY . You are receiving this because you were mentioned.Message ID: @.***>

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chhylp123 commented 1 year ago

It should work. Probably let's have a try first.

hoppo commented 1 year ago

Hi,

Yes, it did work. Thanks for the update - do you need me to do anything on Github?

Cheers, Marie.

On Mon, 28 Nov 2022 at 14:41, chhylp123 @.***> wrote:

It should work. Probably let's have a try first.

— Reply to this email directly, view it on GitHub https://github.com/chhylp123/hifiasm/issues/352#issuecomment-1329111845, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACIDCCV2SNJZAJBCLLY44FLWKSY7XANCNFSM6AAAAAASLNUYOY . You are receiving this because you were mentioned.Message ID: @.***>

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Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior

chhylp123 commented 1 year ago

Thanks. Just curious how does it look like in comparison with the HiFi-only assembly.