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Dee-chen / Tree2gd

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Initail and STEP5 ERROR IN TEST RUN #6

Closed PRTGRWL closed 1 year ago

PRTGRWL commented 1 year ago

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

Dee-chen commented 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.

PRTGRWL commented 1 year ago

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.