search

AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
175 stars 44 forks source link

problem with dbCAN2 #30

Closed jarojasva closed 3 years ago

jarojasva commented 3 years ago

Hello,

I've had a problem with the program. I'm trying to use it with 4 diferent genomes, but at certain point, there were the next errors:

[2021-02-15 11:12:17] Searching CAZymes by dbCAN2... Error: Error: Error: Error: Failed to open binary auxfiles for /mnt/c/Users/AsusLap/Documents/Otros/Apps/METABOLIC-master/dbCAN2/dbCAN-fam-HMMs.txt: use hmmpress first Failed to open binary auxfiles for /mnt/c/Users/AsusLap/Documents/Otros/Apps/METABOLIC-master/dbCAN2/dbCAN-fam-HMMs.txt: use hmmpress first Failed to open binary auxfiles for /mnt/c/Users/AsusLap/Documents/Otros/Apps/METABOLIC-master/dbCAN2/dbCAN-fam-HMMs.txt: use hmmpress first Failed to open binary auxfiles for /mnt/c/Users/AsusLap/Documents/Otros/Apps/METABOLIC-master/dbCAN2/dbCAN-fam-HMMs.txt: use hmmpress first

cat: /mnt/c/Users/AsusLap/Documents/UNAM/Semestre_5/MetabolicProject/Metabolic_Results/intermediate_files/dbCAN2_Files/369_Pseudomonas_A5.feature_protein.dbCAN2.out.dm: No such file or directorycat: cat: /mnt/c/Users/AsusLap/Documents/UNAM/Semestre_5/MetabolicProject/Metabolic_Results/intermediate_files/dbCAN2_Files/183_Paenarthrobacter_A5.feature_protein.dbCAN2.out.dmcat: /mnt/c/Users/AsusLap/Documents/UNAM/Semestre_5/MetabolicProject/Metabolic_Results/intermediate_files/dbCAN2_Files/A1_Pseudomonas_A5.feature_protein.dbCAN2.out.dm: No such file or directory/mnt/c/Users/AsusLap/Documents/UNAM/Semestre_5/MetabolicProject/Metabolic_Results/intermediate_files/dbCAN2_Files/181_Alcanivorax_A5.feature_protein.dbCAN2.out.dm: No such file or directory : No such file or directory [2021-02-15 11:12:19] dbCAN2 searching is done [2021-02-15 11:12:19] Searching MEROPS peptidase... [2021-02-15 11:17:11] MEROPS peptidase searching is done sh: 1: Rscript: Permission denied mv: cannot stat 'METABOLIC_result.xlsx': No such file or directory [2021-02-15 11:17:11] METABOLIC table has been generated [2021-02-15 11:17:11] Drawing element cycling diagrams... sh: 1: Rscript: Permission denied mv: cannot stat '/mnt/c/Users/AsusLap/Documents/UNAM/Semestre_5/MetabolicProject/Metabolic_Results/Output/draw_biogeochem_cycles': No such file or directory rm: cannot remove '/mnt/c/Users/AsusLap/Documents/UNAM/Semestre_5/MetabolicProject/Metabolic_Results/Output': No such file or directory [2021-02-15 11:17:12] Drawing element cycling diagrams finished

So there were no diagrams or other results generated. What should I do?

ChaoLab commented 3 years ago

Hi, It seems that your dbCAN2 is not set up well. From “use hmmpress first”, I guess, maybe, some hmm profiles have not been pressed. Maybe this could be the problem.

All my best!

patriciatran commented 3 years ago

closing because we figured it out by email. The solution is to use hmmpress which is found in the set up .sh script.