Can't open object can't open my reads about simka

[clemaitre]

Hi,

This error occurs when the program does not find the files at the indicated path.
Here, your input file contains only file names (and not absolute paths for instance), in this case, your fasta files must be in the same directory as the input file. Is it the case ?

[FengqingWang0712]

Hi,

This error occurs when the program does not find the files at the indicated path.
Here, your input file contains only file names (and not absolute paths for instance), in this case, your fasta files must be in the same directory as the input file. Is it the case?

Thanks for your reply. It seems not this case. The fasta files and the input files are in the same directory. I ran again after adding absolute paths in input files just now. It showed the same error. Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files?

[clemaitre]

Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files?

No, headers can be anything you want. The error is typical of a "file not found". Are you 100% sure that your files are correctly spelled in the input file and also readable by your system or user ?

[FengqingWang0712]

Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files?

No, headers can be anything you want. The error is typical of a "file not found". Are you 100% sure that your files are correctly spelled in the input file and also readable by your system or user?

Hi. Thanks for your reply.
I checked my data and ran many times using different input.txt files. Luckily, I found the issue finally. It's because of my text format. I use another way to generate the input.txt with the same information and it's working now. I tried using the example txt file and it's proved that my text format is really the reason. It seems that my first text format can't be read by the program. Thanks very much! All the best!

[samuelanyaso]

I encountered the same issue. The program seems to have trouble recognizing plain .txt files. A quick way around this is to convert plain .txt files to UNIX format.
dos2unix input_file.txt

[FengqingWang0712]

I encountered the same issue. The program seems to have trouble recognizing plain .txt files. A quick way around this is to convert plain .txt files to UNIX format.
dos2unix input_file.txt

Thanks very much!