search

junseonghwan / PhylExAnalysis

BSD 2-Clause "Simplified" License
1 stars 0 forks source link

Error from RunInference.py #9

Open cathy-y opened 4 months ago

cathy-y commented 4 months ago

When I try to run the command python3 ../scripts/RunInference.py 1234 bulk.txt sc.txt sc_hp.txt ~/out --local from within the PhylEx folder, I get the error:

libc++abi: terminating due to uncaught exception of type std::invalid_argument: stod: no conversion ./../scripts/RunInference.sh: line 14: 99275 Abort trap: 6 ./run -c ${CONFIG_FILE}

Here are the first five lines for my bulk input:

ID b d major_cn minor_cn chr1_633672 42 48 1 1 chr1_892710 50 64 1 1 chr1_1008682 61 68 1 1 chr1_1317950 63 69 1 1 chr1_1789339 64 75 1 1

For my single-cell input:

ID Cell a d chr10_102349954 GGTCTTGAGGGTGAAC-1 1 1 chr10_102349954 TAAACAGCAGTAGGTG-1 1 1 chr10_102392460 AATGTCCAGCAAGACA-1 1 1 chr10_102392460 AGTAACACAATGCCTA-1 0 1 chr10_102392460 TGTGCGCAGTGCTGTG-1 1 1

For my hyperparameters file:

ID alpha beta delta0 chr1_633672 1 1 0.5 chr1_892710 1 1 0.5 chr1_1008682 1 1 0.5 chr1_1317950 1 1 0.5 chr1_1789339 1 1 0.5

I am running the program from a Mac with an M1 chip, and installed PhylEx successfully using the instructions in the README. Please let me know if you have any additional questions, and thank you in advance!

junseonghwan commented 4 months ago

I cannot reproduce your the problem based on the sample files you provided. One thing that might help is to replace space with tab as the code splits the input files using tabs (\t) rather than space (or white space).

If that doesn't work, can you de-identify mutation information (replace chr_loci with generic s1, s2, etc) and send me the input files? You can email them to me at s2jun.uw AT gmail.com or to seonghwan_jun AT urmc.rochester.edu.