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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Annotating error #31

Closed luishdez35 closed 2 years ago

luishdez35 commented 2 years ago

Error when I run: mitofinder -j Phidippus_adonis_DGF0948 -a Phidippus_adonis_DGF0948.contigs.fasta -r Habronattus_oregonensis_genome.gb -o 5 -p 4 -m 8

Some advice?

Traceback (most recent call last): File "/opt/anaconda3/envs/mitofinder/bin/mitofinder", line 1139, in <module> if check_if_string_in_file(pathtowork + "/geneChecker.log","MiTFi failed.") or (os.stat(pathOfFinalResults+"MiTFi.log").st_size != 0 and not check_if_string_in_file(pathOfFinalResults+"MiTFi.log","hits")) : OSError: [Errno 2] No such file or directory: '/Users/luiscarloshernandez/Desktop/UCEs-Phidippus/Analysis/Mitofinder analisis/Phidippus_adonis_DGF0948/Phidippus_adonis_DGF0948_MitoFinder_mitfi_Final_Results/MiTFi.log' (mitofinder) luiscarloshernandez@MacBook-Air-de-Luis Mitofinder analisis % mitofinder -j Phidippus_adonis_DGF0948_CO1 -a Phidippus_adonis_DGF0948.contigs.fasta -r COI_reference_Phidippus.gb -o 5 -p 4 -m 8

Thanks a lot

RemiAllio commented 2 years ago

Hi !

I can see that you are using the anaconda version of MitoFinder. I don't know who created this version but it's not me ...

My advice would be to install MitoFinder following one of the official installation procedures proposed here.

Sorry for the inconvenience, Best regards, Rémi

luishdez35 commented 2 years ago

Thanks for the reply RemiAllio, I try you suggestion, but I have the same error.

Traceback (most recent call last): File "/Users/luiscarloshernandez/MitoFinder/mitofinder", line 1139, in <module> if check_if_string_in_file(pathtowork + "/geneChecker.log","MiTFi failed.") or (os.stat(pathOfFinalResults+"MiTFi.log").st_size != 0 and not check_if_string_in_file(pathOfFinalResults+"MiTFi.log","hits")) : OSError: [Errno 2] No such file or directory: '/Users/luiscarloshernandez/Desktop/UCEs-Phidippus/Analysis/Mitofinder analisis/Phidippus_adonis_DGF0948/Phidippus_adonis_DGF0948_MitoFinder_mitfi_Final_Results/MiTFi.log'

It seems that mitfi can't write the log file, and it doesn't give me the output files that it should.

Thanks for your support

luishdez35 commented 2 years ago

SOLVED, I put the contigs inside the folder test_case in Mitofinder directory, and work fine, I don't know why in others directory doesn't work,