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simroux / Inovirus

Set of scripts and data used to detect putative inovirus sequences and/or taxonomically classify them.
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error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory ... in Example_files #5

Open gucedac opened 2 years ago

gucedac commented 2 years ago

When I run the Get_inovirus_prediction_score_from_gff_fragments.pl script, it works at the beginning of the process, it creates the Tmp_input.csv file, but then this file can not be recognizes for the next steps ...

[...] Ga0128599_102376 73621 - 74886 is in the fragment DUF1329 // // DUF1329 is not unexpected Ga0128599_102377 75473 - 76210 is in the fragment Asp_Glu_race // // Ga0128599_102378 76251 - 77009 is in the fragment adh_short_C2 // // Ga0128599_102379 77060 - 78535 is in the fragment Amidase // // Ga0128599_102380 78579 - 79964 is in the fragment Amidase // // Ga0128599_102381 79961 - 81286 is in the fragment // // Ga0128599_102382 81308 - 82333 is in the fragment FAD_binding_6 // // Ga0128599_102383 83014 - 84018 is in the fragment AraC_binding_2 // // Ga0128599_102384 84193 - 85530 is in the fragment Aromatic_hydrox // // Ga0128599_102385 85677 - 86501 is in the fragment Abhydrolase_1 // // Ga0128599_102386 86548 - 86991 is in the fragment Lipocalin_5 // // Ga0128599_102387 86988 - 87866 is in the fragment Glyoxalase // // Ga0128599_102388 87990 - 89093 is in the fragment ADH_N // // Ga0128599_102389 89337 - 89615 is in the fragment // // Ga0128599_102390 89696 - 90649 is in the fragment LigB // // Rscript run_predict.R Example_files/2731957639_expected_results/Tmp_input.csv Example_files/2731957639_expected_results/Tmp_output.csv InovirusModel.RData /media/guillermo/Work/miniconda3/envs/inovirus_detector/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory

Can't open 'Example_files/2731957639_expected_results/Tmp_output.csv' for reading: 'No such file or directory' at Get_inovirus_prediction_score_from_gff_fragments.pl line 274

Any idea about what is ti happening? Thank you

simroux commented 2 years ago

Looks like R is not happy (this is what the "R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory" means). I think I have fixed it in the past by installing "readline" via conda (https://anaconda.org/anaconda/readline). If you manage to do that with mamba, then you can delete the output directory and relaunch the script, and see if you get the same error ?

gucedac commented 2 years ago

Looks like R is not happy (this is what the "R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory" means). I think I have fixed it in the past by installing "readline" via conda (https://anaconda.org/anaconda/readline). If you manage to do that with mamba, then you can delete the output directory and relaunch the script, and see if you get the same error ?

I use mamba to install readline but I got the same error

simroux commented 2 years ago

Arg.. It may be that a specific version of readline has to be installed, see e.g.: https://github.com/bioconda/bioconda-recipes/issues/13439 https://www.reddit.com/r/Rlanguage/comments/77plyj/anaconda_install_of_r_via_ressentials_not/

gucedac commented 2 years ago

Arg.. It may be that a specific version of readline has to be installed, see e.g.: bioconda/bioconda-recipes#13439 https://www.reddit.com/r/Rlanguage/comments/77plyj/anaconda_install_of_r_via_ressentials_not/ Thanks a lot To me worked updating conda with this command: conda update --all