Open mattiarag99 opened 6 months ago
Hi Mattia, Can you share the commande line that are you using? I understand that you used the -X option?? Can you share the first part of your CSV??
Dear Jorge, thanks a lot for your quick answer
This is the command line:
SPdel.py caeliferadatasetforspedelNOBIN.fasta -t caeliferadefNOBIN_tree.nwk -C ABGD_JK_INIT,ABGD_JK_REC,ASAP_JK,ASAP_K2,BIN,ABGD_JK_INIT_1,ABGD_JK_REC_1,ASAP_JK_1,ASAP_K2_1,BIN_1 -X FAKEFILECSVCAELIF1.csv
I have used just pre-calculated species delimitation clusters using different methods, and also different combinations of parameters for each method. For this reason you can read different variants of ABGD, ASAP and BIN, I don't know if this is a problem. I also inserted a newick tree, but without using GMYC or PTP, for now, even if I need to use them in the definitive run, which would include 13 delimitation methods/combinations of parameters (for this reason the csv file is named as FAKE..).
Here the first part of my CSV file
name,ABGD_JK_INIT,ABGD_JK_REC,ASAP_JK,ASAP_K2,BIN,ABGD_JK_INIT_1,ABGD_JK_REC_1,ASAP_JK_1,ASAP_K2_1,BIN_1
Acinipe_ignatii_IBIOR231-22,Group[76],MOTU_GROUP[76],MOTU_SUB[85],MOTU_SUB[76],MOTU_AER2325,Group[76],MOTU_GROUP[76],MOTU_SUB[85],MOTU_SUB[76],MOTU_AER2325
Acinipe_ignatii_IBIOR232-22,Group[76],MOTU_GROUP[76],MOTU_SUB[85],MOTU_SUB[76],MOTU_AER2325,Group[76],MOTU_GROUP[76],MOTU_SUB[85],MOTU_SUB[76],MOTU_AER2325
Acinipe_segurensis_MEDOR004-23,Group[83],MOTU_GROUP[83],MOTU_SUB[92],MOTU_SUB[83],MOTU_AFG2876,Group[83],MOTU_GROUP[83],MOTU_SUB[92],MOTU_SUB[83],MOTU_AFG2876
Acinipe_segurensis_MEDOR575-23,Group[125],MOTU_GROUP[125],MOTU_SUB[136],MOTU_SUB[126],MOTU_AFG2875,Group[125],MOTU_GROUP[125],MOTU_SUB[136],MOTU_SUB[126],MOTU_AFG2875
Acinipe_segurensis_MEDOR576-23,Group[125],MOTU_GROUP[125],MOTU_SUB[136],MOTU_SUB[126],MOTU_AFG2875,Group[125],MOTU_GROUP[125],MOTU_SUB[136],MOTU_SUB[126],MOTU_AFG2875
Acinipe_segurensis_MEDOR577-23,Group[83],MOTU_GROUP[83],MOTU_SUB[92],MOTU_SUB[83],MOTU_AFG2876,Group[83],MOTU_GROUP[83],MOTU_SUB[92],MOTU_SUB[83],MOTU_AFG2876
Acinipe_segurensis_MEDOR578-23,Group[83],MOTU_GROUP[83],MOTU_SUB[92],MOTU_SUB[83],MOTU_AFG2876,Group[83],MOTU_GROUP[83],MOTU_SUB[92],MOTU_SUB[83],MOTU_AFG2876
Acrida_sp_MEDOR314-23,Group[111],MOTU_GROUP[111],MOTU_SUB[121],MOTU_SUB[112],MOTU_ACN8433,Group[111],MOTU_GROUP[111],MOTU_SUB[121],MOTU_SUB[112],MOTU_ACN8433
Acrida_ungarica_GBORT781-15,Group[39],MOTU_GROUP[39],MOTU_SUB[47],MOTU_SUB[40],MOTU_AAP4333,Group[39],MOTU_GROUP[39],MOTU_SUB[47],MOTU_SUB[40],MOTU_AAP4333
Thanks a lot for the help Best Mattia
Dear Mattia, Thanks, I can see some possible sources of the error.
In your CSV:
Let me know if some of these work.
Best
Dear Jorge, thanks for the help I forgot to mention that I had already run an analysis with the same dataset (and specimens and MOTU name) a week ago, but without using so many methods. The tool correctly created a tree with delimitation bars, but without the consensus part, giving me a warning concerning the fact that for reaching a consensus I needed to get more methods.
For this reason, I suppose the error is in the part concerning the production of a consensus. Could be?
As I am not familiar with writing code, in the meantime I asked chatgpt about the error, and it suggested me to modify the code at line 648, chainging from record.id = newname + '' + k to record.id = str(newname) + '' + str(k)
Otherwise, I was wondering if maybe the presence of underscores in the column titles could be the main issue, but I dont know
Sorry for the long message, it is just cause this is the last step of a work I have to give in few time and I hope to find the solution Best Mattia
p.s. btw I am trying to run with your suggestion, thanks again
HI Mattia, probably your results were inclonclusive (maybe a discrepant results between analysis) so the recomendation is to include more analysis, but it's not always a solution.
For check that you can try SPdel.py caeliferadatasetforspedelNOBIN.fasta -t caeliferadefNOBIN_tree.nwk -C ABGD_JK_INIT,ABGD_JK_REC,ASAP_JK,ASAP_K2,BIN,ABGD_JK_INIT_1,ABGD_JK_REC_1,ASAP_JK_1,ASAP_K2_1,BIN_1 -X FAKEFILECSVCAELIF1.csv -nocons
The option -nocons will draw the tree but will not calculate the consensus.
Dear Jorge, I tried to run the analysis with your suggestions, but sadly, while elaborating the consensus, it gives me the same error I try to run the analysis without consensus Have you ever encountered similar issues for the consensus draw? Thanks a lot again
p.s. the -nocons flag will allow to produce the tree with bars anyway? Ofc without consensus
p.s. is there an option to run the analysis in multi-threads?
p.s. the -nocons flag will allow to produce the tree with bars anyway? Ofc without consensus
Yes, it's very useful to check te results
p.s. is there an option to run the analysis in multi-threads?
Not for now
Dear Jorge, I tried to run the analysis with your suggestions, but sadly, while elaborating the consensus, it gives me the same error I try to run the analysis without consensus Have you ever encountered similar issues for the consensus draw? Thanks a lot again
Can you share your files to test here?? Could be via email (jramirezma@unmsm.edu.pe)
Dear Jorge, the analysis without consensus is still running, but of course I will send you my files Thanks for your kind help, just sent an email Best regards Mattia
Dear all, I am reporting a problem with the creation of Consensus clusters. I was running SPdel.py with only pre-elaborated clusters of 14 different species delimitation methods (combinations of parameters), but once arrived at the creation of Consensus clusters and the svg tree, the command line report an error:
"_Traceback (most recent call last):
File "/home/student/miniconda3/envs/spdel/bin/SPdel.py", line 1212, in
File "/home/student/miniconda3/envs/spdel/bin/SPdel.py", line 1203, in main
File "/home/student/miniconda3/envs/spdel/bin/SPdel.py", line 991, in run
File "/home/student/miniconda3/envs/spdel/bin/SPdel.py", line 896, in run_comparison
File "/home/student/miniconda3/envs/spdel/bin/SPdel.py", line 648, in MOTU_renameFasta_Compare
TypeError: unsupported operand type(s) for +: 'float' and 'str'_"
May I ask for help for correcting this issue? Thanks a lot Best Mattia