run completes but results without haplotypes

[jokelley]

I am running hifiasm, it seems to complete (see below). The bin files are created: -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 16865946225 May 26 17:04 Oamb.asm.ec.bin -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 33221876 May 26 17:04 Oamb.asm.ovlp.reverse.bin -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 33273032 May 26 17:04 Oamb.asm.ovlp.source.bin

there is nothing in any other file.

Outfile:

[M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 82; peak_het: -1 [M::ha_ct_shrink::280917.08715.88] ==> counted 61786409 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1848882850 minimizers [M::ha_pt_gen::281172.18615.88] ==> indexed 415712730 positions, counted 61786409 distinct minimizer k-mers [M::ha_assemble::307317.290*15.89@81.589GB] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 1231 [M::ha_print_ovlp_stat] # strong overlaps: 173 [M::ha_print_ovlp_stat] # weak overlaps: 1058 [M::ha_print_ovlp_stat] # exact overlaps: 183 [M::ha_print_ovlp_stat] # inexact overlaps: 1048 [M::ha_print_ovlp_stat] # overlaps without large indels: 1231 [M::ha_print_ovlp_stat] # reverse overlaps: 13 [M::ha_opt_update_cov_min] updated max_n_chain to 410 Writing reads to disk... Reads has been written. Writing ma_hit_ts to disk... ma_hit_ts has been written. Writing ma_hit_ts to disk... ma_hit_ts has been written. bin files have been written. [M::purge_dups] homozygous read coverage threshold: 81 [M::purge_dups] purge duplication coverage threshold: 102 Writing raw unitig GFA to disk... Writing processed unitig GFA to disk... [M::purge_dups] homozygous read coverage threshold: 81 [M::purge_dups] purge duplication coverage threshold: 102 [M::mc_solve:: # edges: 0] [M::mc_solve_core_adv::0.000] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [68, infinity] Writing primary contig GFA to disk... Writing alternate contig GFA to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.19.4-r575 [M::main] CMD: hifiasm -o Oamb.asm --primary -t 16 Oamber_PacBio.fastq.gz [M::main] Real time: 307373.672 sec; CPU: 4882249.274 sec; Peak RSS: 81.589 GB

[chhylp123]

Could you please rerun hifiasm with bin files and check if there are some outputs? It should be pretty fast.

[jokelley]

Reran it, still didn't write any outputs: Reads has been loaded. Loading ma_hit_ts from disk... ma_hit_ts has been read. Loading ma_hit_ts from disk... ma_hit_ts has been read. [M::ha_assemble::17.146*1.00] ==> loaded corrected reads and overlaps from disk [M::ha_opt_update_cov_min] updated max_n_chain to 410 [M::purge_dups] homozygous read coverage threshold: 81 [M::purge_dups] purge duplication coverage threshold: 102 Writing raw unitig GFA to disk... Writing processed unitig GFA to disk... [M::purge_dups] homozygous read coverage threshold: 81 [M::purge_dups] purge duplication coverage threshold: 102 [M::mc_solve:: # edges: 0] [M::mc_solve_core_adv::0.000] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [68, infinity] Writing primary contig GFA to disk... Writing alternate contig GFA to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.19.4-r575 [M::main] CMD: hifiasm -o Oamb.asm --primary -t 16 Oamber_PacBio.fastq.gz [M::main] Real time: 32.876 sec; CPU: 95.191 sec; Peak RSS: 18.113 GB

[chhylp123]

The log file shows hifiasm is ok. Could you please check if it outputs gfa to elsewehre?

[jokelley]

They don't go anywhere else, I tried running it entirely in a different location. Ran for 3 days and generated the same issue with not writing any output except the bin files. Any suggestions on what else to do?

-rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.a_ctg.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.a_ctg.lowQ.bed -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.a_ctg.noseq.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 16865946225 Jun 1 20:40 Oamb.asm.ec.bin -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 33221876 Jun 1 20:40 Oamb.asm.ovlp.reverse.bin -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 33273032 Jun 1 20:40 Oamb.asm.ovlp.source.bin -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.p_ctg.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.p_ctg.lowQ.bed -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.p_ctg.noseq.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.p_utg.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.p_utg.lowQ.bed -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.p_utg.noseq.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.r_utg.gfa -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.r_utg.lowQ.bed -rw-r----- 1 joanna.l.kelley its_p_sys_ur_kam-kelley 0 Jun 1 20:40 Oamb.asm.r_utg.noseq.gfa

[chhylp123]

These gfa files, like Oamb.asm.p_ctg.gfa, are the outputs. Which types of outputs would you like to get?

[jokelley]

Sorry the formatting wasn’t clear, the files are all empty. They are created but never written to. The log and bin files are fine and this isn’t a space or memory issue on my cluster. On Jun 2, 2023, at 3:19 PM, chhylp123 @.***> wrote: These gfa files, like Oamb.asm.p_ctg.gfa, are the outputs. Which types of outputs would you like to get?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

[chhylp123]

It shouldn't happen... Is it possible that you can share the bin files with us? I still feel like it is not the problem of hifiasm.

[jokelley]

Absolutely, how should I get them to you?

On Fri, Jun 2, 2023 at 8:18 PM chhylp123 @.***> wrote:

It shouldn't happen... Is it possible that you can share the bin files with us? I still feel like it is not the problem of hifiasm.

— Reply to this email directly, view it on GitHub https://github.com/chhylp123/hifiasm/issues/459#issuecomment-1574134912, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQA5SU4BGWTYYA36AJV6YTXJIU6ZANCNFSM6AAAAAAYQ7QZCI . You are receiving this because you authored the thread.Message ID: @.***>

[chhylp123]

Sorry for the late reply. Could you please share with me using onedrive or goolgdrive?