Closed PRTGRWL closed 1 year ago
Hello, after checking, the problem you reported should be due to the fact that trimAl software is not installed. In v1.0.41 of Tree2gd, I added the function of using trimAl to filter the sequence alignment results. Unlike other software, I have not added the precompiled trimAl in the Tree2gd installation package. At present, you can use conda to install trimAl, or download the pre compiled version I just uploaded and add it to your PATH( https://github.com/Dee-chen/Tree2gd/tree/master/tree2gd/software/trimal )。 After that, it can be used normally.
I'll be fixing the bugs I've collected so far in the near future, uploading a full new version of Tree2gd in a few days, and then you'll be able to use Tree2gd normally through pypi updates.
Again, I'm sorry for causing you trouble with Tree2gd analysis.
Thank you so much for the quick response. As per your suggestion, right now , I installed Trimal through conda and it is working fine now.
Hi..
I am using Tree2GD:A pipeline for WGD V1.0.41 version. I am working on example_data.
Firstly just for information regarding initial ERROR which was resolved manually Initial Error explained:- I got an Error of permission denied when pipelines moves towards using software. So I have to manually provide permission to all the tools in software by chmod 777. Then the pipelines moves forward
Second ERROR : At step 5
Start gene pairs kaks calculation. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/preeti.agarwal/anaconda3/envs/t2g/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/preeti.agarwal/anaconda3/envs/t2g/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/home/preeti.agarwal/.local/lib/python3.8/site-packages/tree2gd/kaks.py", line 84, in run_ks sub_sh(args[0],args[1],args[2],args[3],args[4],args[5],args[6]) File "/home/preeti.agarwal/.local/lib/python3.8/site-packages/tree2gd/kaks.py", line 123, in sub_sh Fasta2AXT(pair[2]+"-"+pair[3]+".filted.cds_aln",pair[2]+"-"+pair[3]+".cds_aln.axt") File "/home/preeti.agarwal/.local/lib/python3.8/site-packages/tree2gd/kaks.py", line 137, in Fasta2AXT for s in read_fasta_file(input): File "/home/preeti.agarwal/.local/lib/python3.8/site-packages/tree2gd/seq.py", line 63, in read_fasta_file fl = open(filename,"r") FileNotFoundError: [Errno 2] No such file or directory: 'evm.model.supercontig_85.105-evm.model.supercontig_85.106.filted.cds_aln' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/preeti.agarwal/.local/bin/Tree2gd", line 8, in
sys.exit(main())
File "/home/preeti.agarwal/.local/lib/python3.8/site-packages/tree2gd_main.py", line 268, in main
run_kaks(sp_list,step1out,args,cf,step4out,step5out,gene_pairs_idmap)
File "/home/preeti.agarwal/.local/lib/python3.8/site-packages/tree2gd/kaks.py", line 63, in run_kaks
sh_pool.map(run_ks,arg_list)
File "/home/preeti.agarwal/anaconda3/envs/t2g/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/preeti.agarwal/anaconda3/envs/t2g/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'evm.model.supercontig_85.105-evm.model.supercontig_85.106.filted.cds_aln'
(END)
Here to mention that I am using syntax $Tree2gd_test only. Then why am I getting this error