fail to run set up #57
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Hello @xushaoyi , Thanks for your interest in BackBLAST. Version 2 is still under development and is not yet stable or fully documented, but I'm happy to hear that you'd like to give it a try. I think the easiest first course of action is to see if you can get the built-in test data to run successfully. Would you mind giving that a try? Here is how:
mkdir -p testing/outputs
# Make sure your backblast conda env is activated before you run the test
backblast run testing/inputs/config.yaml testing/outputs --notemp
cmp testing/outputs/blast/combine_blast_tables/blast_tables_combined.csv \
testing/outputs_expected/blast/combine_blast_tables/blast_tables_combined.csv
# You will get an error message if the two files do not perfectly match
Let me know if this works, or if it fails, then send me a screenshot, and we can troubleshoot from there. Thanks. |
thanks for your reply！ I tried what you suggessted, and at 2nd step, it was failed. the detail was as follows： |
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Hi @xushaoyi , This is really helpful -- thanks. It looks like your BackBLAST install folder is not being recognized properly. Can you confirm if Thanks! |
oh,it seems it was not installed, since the output is:"-bash: realpath: command not found". so, how can install it? thanks very much! |
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@xushaoyi What type of linux system are you running? For example, are you using debian? Also, are you using a HPC cluster or on an individual server? I had not realized that For now, try running |
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P.S. Otherwise, you can just install |
hi,readlink seems work,so would you mind update the code? thanks so much ! |
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@xushaoyi Thanks for your prompt response. I did some more background reading and found that Until then, I'd recommend trying to install |
dear author, finally I was successfully installed, and the test finished, details as follows: but when I run my data, something again seems wrong, it was so sad... can you help me ? thansk so much! |
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Hi @xushaoyi , My apologies for the delayed response -- other deadlines came up on this end that prevented me from getting to the code. I'm glad you found the -U and -T flags as manual workaround for locating the script path. Are you using BackBLAST version 2.0.0-alpha3? There was an environment path issue in that version that caused issues with phylogenetic tree generation. The issue was corrected in version 2.0.0-alpha4 (https://github.com/LeeBergstrand/BackBLAST_Reciprocal_BLAST/releases) You might need to update to the latest version to continue. |
ok.I will try, thanks! also, I have a non-technonical quetion, how can I get the faa file for the reference genome? it seems the data on NCBI was very limited. only few representive genomes were availble for that data. |
hi，sorry to disturb you again, I updated the software as you suggested, but when I run the code, something still wrong...so sad.. |
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Hi @xushaoyi , It looks like the script is failing with a cryptic error message when loading the phylogenetic tree. Based on the log, it must be failing when running the I assume this must be due to an issue with the conda environment. From Bash, can you activate your backblast conda environment and then run Based on the log, you are going to run into a second error later because of not having Sorry you've had issues with the code so far, but I'm happy to see that you are close to getting it to work end-to-end. Only one step left to go. |
sorry to reply you late, here is the details of conda list: for the second question, I have changed the path to the absolute system path, but the error seems still occur. please help me, thanks sooo much! Name Version Build Channel_libgcc_mutex 0.1 conda_forge conda-forge |
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@xushaoyi Sorry for the delay, and thanks for sending these details! I'll take a look at this soon and will get back to you. -Jackson |
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@xushaoyi I apologize for not being able to get back to you about BackBLAST yet -- I am busy preparing for my PhD defence next week, and debugging this issue could take some time. I hope to get back to you after my defence and revisions are complete. |
thanks for your kind help! it's ok, do it when if it's convinent for you, I can do other analysis first! thanks again for your patience! Wish you all the best! |
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Thanks, I appreciate it. :-) |
dear author, I used install manual in this website (https://zenodo.org/record/3697265#.XykIRigzbic) and create the backblast env by conda. but when I want to use backblast setup command, it was failed. and the error was as follows:
I don't know how to solve it, so maybe do you have any suggestions? thanks !
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