Bug: macs3 hmmratac crashes with --save-likelihoods option

[mosheolshansky-dot]

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Expected behavior
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System (please complete the following information):

• OS: [e.g. Linux, Mac OSX] [note: Windows NOT supported]
• Python version [e.g. 3.7.1]
• Numpy version [e.g. 1.17.0]
• MACS Version [e.g. 2.2.4]

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[mosheolshansky-dot]

Below is my command:

hmmratac -f BEDPE --keep-duplicates -u 100 -l 50 -c 10 --save-states --save-likelihoods --pileup-short --buffer-size 10000000 -i HPDE_ATAC_DMSO_1_auto.bed HPDE_ATAC_DMSO_2_auto.bed HPDE_ATAC_DMSO_3_auto.bed -n HPDE_auto_short

It first runs all right, but then it crashes withe the below error (I include a few lines of output before the crash as well):

INFO @ 06 Nov 2025 15:38:16: [10984 MB] # decoding 115000...
INFO @ 06 Nov 2025 15:38:18: [10984 MB] # decoding 116000...
INFO @ 06 Nov 2025 15:38:20: [10984 MB] # predicted_proba files written...
INFO @ 06 Nov 2025 15:38:20: [10984 MB] # Write the output...
INFO @ 06 Nov 2025 15:38:20: [10984 MB] # Write the likelihoods for each states into three bedGraph files HPDE_auto_short_open.bdg, HPDE_auto_short_nuc.bdg, and HPDE_auto_short_bg.bdg
Traceback (most recent call last):
File "/home/molshansky/.local/bin/macs3", line 983, in
main()
File "/home/molshansky/.local/bin/macs3", line 97, in main
run( args )
File "/home/molshansky/.local/lib/python3.10/site-packages/MACS3/Commands/hmmratac_cmd.py", line 444, in run
save_proba_to_bedGraph( predicted_proba_file, options.hmm_binsize, open_state_bdg_fhd, nuc_state_bdg_fhd, bg_state_bdg_fhd, i_open_region, i_nucleosomal_region, i_background_region )
File "/home/molshansky/.local/lib/python3.10/site-packages/MACS3/Commands/hmmratac_cmd.py", line 470, in save_proba_to_bedGraph
open_state_bdg_file = bedGraphIO( open_state_bdg_file )
TypeError: Argument 'bedGraph_filename' has incorrect type (expected str, got _io.TextIOWrapper)

Thank you,

Moshe Olshansky
Baker Heart & Diabetes Institute
Melbourne, VIC, Australia

[taoliu]

@mosheolshansky-dot This has been fixed in #685 and should be included in version 3.0.3 https://github.com/macs3-project/MACS/releases/tag/v3.0.3.

[mosheolshansky-dot]

Thank you very much!

…

On Fri, Nov 7, 2025 at 5:28 AM Tao Liu (τν) ***@***.***> wrote: *taoliu* left a comment (macs3-project/MACS#713) <#713 (comment)> @mosheolshansky-dot <https://github.com/mosheolshansky-dot> This has been fixed in #685 <#685> and should be included in version 3.0.3 https://github.com/macs3-project/MACS/releases/tag/v3.0.3. — Reply to this email directly, view it on GitHub <#713 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BZY5UR7JXMZ2X2VUUVQU55T33OHNPAVCNFSM6AAAAACLJJMX7OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIOJYG44TKMZQHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>