Stuck at Recombination hit list...

[GRGong]

Thanks for the magic tool! However, I met an issue when I use this tool for some genome assemblies. The tool stucked at "Recombination hit list..." stage. Please help me to figure it out. Here is a example log:

Internal pipeline statistics summary:

Query model(s): 1 (933 nodes)
Target sequences: 10042 (1643500208 residues searched)
Residues passing SSV filter: 230121808 (0.14); expected (0.02)
Residues passing bias filter: 137319152 (0.0836); expected (0.02)
Residues passing Vit filter: 23211691 (0.0141); expected (0.003)
Residues passing Fwd filter: 1005657 (0.000612); expected (3e-05)
Total number of hits: 120 (5.89e-05)

CPU time: 284.11u 0.93s 00:04:45.04 Elapsed: 00:00:03.61

Mc/sec: 424531.06

//
[ok]
284.17user 1.04system 0:03.78elapsed 7527%CPU (0avgtext+0avgdata 1324568maxresident)k
0inputs+64outputs (0major+424205minor)pagefaults 0swaps
2023-04-28 17:20:24,357 Functions.py:INFO run_nhmmer use 3.792 seconds

NHMMER program is complete.

2023-04-28 17:20:24,357 nhmmer.py:INFO ###Program nhmmer.py finish###
2023-04-28 17:20:24,407 Functions.py:INFO ###FindOR program starts running###
2023-04-28 17:20:24,408 Functions.py:INFO function platform_info() is running
The system you use is Linux.
Python3 is used.
2023-04-28 17:20:24,411 Functions.py:INFO platform_info use 0.003 seconds
Process nhmmer output file...
2023-04-28 17:20:24,411 Functions.py:INFO function proc_nhmmer_out() is running
2023-04-28 17:20:24,411 Functions.py:INFO 2 truncated gene(s) was discovered
2023-04-28 17:20:24,412 Functions.py:INFO proc_nhmmer_out use 0.001 seconds
Extract cds from genomic file...
2023-04-28 17:20:24,412 Functions.py:INFO function extract_cds() is running
2023-04-28 17:20:26,673 Functions.py:INFO extract_cds use 2.262 seconds
Find ATG and STOP codons for each sequence...
2023-04-28 17:20:26,673 Functions.py:INFO function find_cds() is running
2023-04-28 17:20:26,779 Functions.py:INFO find_cds use 0.105 seconds
Write data to file...
2023-04-28 17:20:26,786 Functions.py:INFO Merge pseudogene fragement
2023-04-28 17:20:26,787 Functions.py:INFO ###The result as follows###
2023-04-28 17:20:26,787 Functions.py:INFO Clarias_batrachus processing completed
2023-04-28 17:20:26,787 Functions.py:INFO 118 OR fragments found by nhmmer.
2023-04-28 17:20:26,787 Functions.py:INFO 91 potential functional ORs were discover.
2023-04-28 17:20:26,787 Functions.py:INFO -48 pseudogenes fragment were merged
2023-04-28 17:20:26,787 Functions.py:INFO 66 potential pseudogene ORs were discover.
2023-04-28 17:20:26,787 Functions.py:INFO 2 pseudogenes cause by too short sequence length.
2023-04-28 17:20:26,787 Functions.py:INFO 1 pseudogenes cause by insert or delect base.
2023-04-28 17:20:26,787 Functions.py:INFO 63 pseudogenes cause by contains termination codons.
2023-04-28 17:20:26,787 Functions.py:INFO ###The program finish###
2023-04-28 17:20:26,787 FindOR.py:INFO ###Program FindOR.py finish###
2023-04-28 17:20:26,831 Functions.py:INFO ###IdentityFunc program starts running###
2023-04-28 17:20:26,831 Functions.py:INFO function platform_info() is running
The system you use is Linux.
Python3 is used.
2023-04-28 17:20:26,835 Functions.py:INFO platform_info use 0.003 seconds
Process hit sequence file...
2023-04-28 17:20:26,835 Functions.py:INFO function refact_hitfile() is running
2023-04-28 17:20:26,835 Functions.py:INFO refact_hitfile use 0.000 seconds
Recombination hit list...
2023-04-28 17:20:26,835 Functions.py:INFO function refact_list() is running

[ToHanwei]

Thank you for your feedback.
Based on your log file, I have located the function that may be causing the problem.
https://github.com/ToHanwei/Genome2OR/blob/639aff37aa7c8a8cc04f5f6ce0ea4590d7346530/scripts/src/Functions.py#L761
The main function of this step is to merge the hit sequence with the template sequence and perform multiple sequence alignment. In order to speed up this process, I use the multiprocessing module to do pseudo-parallel processing. In your case, the process may be blocked for some unknown reason.

[ToHanwei]

I have solved this problem in the new version.

[GRGong]

Thank you very much! It did work.