onehic.py error : no such file png/info.txt

[pdru]

Hello, I like very well AutoHiC with 3d-dna, but I want to improve your assembly pipeline using YAHS but I have some problems.

I already try to run onehic with peanut example to test the pipeline that seems to work well on my computer

python3.9 onehic.py -hic test/peanut.hic -asy test/peanut.assembly -autohic $PWD -p models/chr_model.pth -t 40 -out test/onehic_2024_11_18 2>&1 |tee onehic_test.$(date +%F).stdout

So with my data, I am trying to run onehic.py after yahs mapping : mapping from yahs has been done with Arima_pipeline and convert to .hic following onehic protocol, as well the genome converted from fasta to assembly.

tree onehic_Bs_trim/

              
 onehic_Bs_trim/
├── assembly_after_yahs.assembly
└── mapped_hic_after_yahs.hic
0 directories, 2 files

So I launch the pipeline :

python3.9 onehic.py -hic onehic_Bs_trim/mapped_hic_after_yahs.hic -asy onehic_Bs_trim/assembly_after_yahs.assembly -autohic /scratch1/genomes/dru/AutoHiC-1.3.3 -p models/chr_model.pth -out /scratch1/genomes/dru/AutoHiC-1.3.3/onehic_Bs_trim/results_onehic 2>&1 |tee onehic_Bs_trim/onehic.$(date +%F).log

after launching this command (following the protocol...), this command stops with an error :

a │ ) │ │
│ │ ) │ │
│ │ ) │ │
│ │ model_cfg = '//scratch1/genomes/dru/AutoHiC-1.3.3/src/models/cfgs/error_model.py' │ │
│ │ out_path = 'onehic_Bs_trim/results_onehic' │ │
│ │ pretrained_model = 'models/chr_model.pth' │ │
│ │ score = 0.9 │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
FileNotFoundError: [Errno 2] No such file or directory: 'onehic_Bs_trim/results_onehic/png/info.txt'

I obtain

tree onehic_Bs_trim/

onehic_Bs_trim/
├── assembly_after_yahs.assembly
├── mapped_hic_after_yahs.hic
├── onehic.2024-11-22.log
└── results_onehic
    └── png
        ├── 1000
        ├── 10000
        ├── 100000
        ├── 1000000
        ├── 25000
        ├── 250000
        ├── 2500000
        ├── 5000
        ├── 50000
        └── 500000

12 directories, 3 files

Do you have an idea of what's wrong with these data ?

[Jwindler]

you cmd -p models/chr_model.pth > -p models/error_model.pth , and you may upload onehic.2024-11-22.log for check

[pdru]

Yes, here is log file :
onehic.2024-11-22.log

I have already tried with error_model.pth that yields exactly the same error... (info.txt not found...

I did not understand the difference between the 2 models....

So now, I create a docker environment to prepare one hic, and prepare environment, and now just run this command :
(onehic) root@7705c39a0ac1:/AutoHiC#
python3.9 onehic.py -hic /home/autohic/onehic_Bs_trim/mapped_hic_after_yahs.hic -asy /home/autohic/onehic_Bs_trim/assembly_after_yahs.assembly -autohic /AutoHiC -p /home/autohic/models/error_model.pth -out /home/autohic/onehic_Bs_trim/results_onehic.$(date +%F) 2>&1 |tee /home/autohic/onehic_Bs_trim/onehic.$(date +%F).log
and :
│ │ ) │ │
│ │ ) │ │
│ │ model_cfg = '/AutoHiC/src/models/cfgs/error_model.py' │ │
│ │ out_path = '/home/autohic/onehic_Bs_trim/results_onehic.2024-11-23' │ │
│ │ pretrained_model = '/home/autohic/models/error_model.pth' │ │
│ │ score = 0.9 │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
FileNotFoundError: [Errno 2] No such file or directory: '/home/autohic/onehic_Bs_trim/results_onehic.2024-11-23/png/info.txt'
(autohic) root@7705c39a0ac1:/AutoHiC#

`
and here the log file
onehic.2024-11-23.log

[Jwindler]

[Jwindler]

maybe -out you should set new dir

[pdru]

Sorry for boring you....
Same and immediate error... as it does not read well assembly file or hic file....
info.txt is not created...
python3.9 onehic.py -hic /home/autohic/onehic_Bs_trim/mapped_hic_after_yahs.hic -asy /home/autohic/onehic_Bs_trim/assembly_after_yahs.assembly -autohic /AutoHiC -p /home/autohic/models/error_model.pth -out /home/autohic/new.results_onehic.$(date +%F) 2>&1 |tee /home/autohic/new.results_onehic.$(date +%F).log

log file :
new.results_onehic.2024-11-23.log

assembly looks like :
assembly_after_yahs.zip

[Jwindler]

i think your .asy is not match .hic, maybe you should ref https://github.com/Jwindler/AutoHiC/blob/main/example/other_tools.md to prepare .hic and .asy

[pdru]

I already follow this page for converting to hic and asy, will try other solutions to obtain valid bam file. Thank you. I'll keep you informed of the issue.

[Jwindler]

if the .hic file no too big, you can send for me to check.

[pdru]

sorry, too big....

[pdru]

so, I confirm : bam output from yahs / arima pipeline does not fit to Onehic. I use another pipeline, HapHiC, to onehic, and it works well. Something's worrying : genome.assembly output is not as compact as AutoHiC (284 fragments...), and I have to pass another Autohic to obtain chr level genome...You did not cite if it is worth to make the 3d-dna post-review pipeline I used to obtain these 284 scaffolds....

run 3d-dna to get fasta

bash run-asm-pipeline-post-review.sh -r adjusted.assembly genome.fasta merged_nodups.txt

Have I done something wrong ?