"ValueError: Input AGPs do not have the same set of components"

[ysawires12345678]

Hello, I ran RagTag on plasmid contigs (correct; scaffold) and output files went to ragtag_output directory. this seems it worked (used one refernce sequence) fine (I received the nice Goodbye). However, when I ran merge using this command:

ragtag.py merge ABDU01.1-plasmid.txt out_*/*.agp other.map.agp -u

I received the above error (copied from the last line. I think I'm putting the wrong command or in the wrong directory? would you please be able to help me with this Thank You

[malonge]

Hi there,

Your command seems to be off because there should be a fasta file instead of a txt file. Please read the Wiki and let me know if you still have any questions.

Thanks, Mike

[ysawires12345678]

Thanks for your response, it is a ".fasta" format file but opened in notepad. I repeated the process with 2 reference sequence. I ran "correct" against one and scaffold against both. when I ran scaffold with the second reference it came back with this message (though the 2 references share 99% identity) "RuntimeError: There are no useful alignments. Check output alignment files" and there was no .agp file in the out_2 folder.

[malonge]

Hi there,

So I will first comment on the original error: ValueError: Input AGPs do not have the same set of components

In order to use merge, the AGPs file must contain the same set of components. In other words, the AGP files must be ordering and orienting the exact same set of sequences. So to address this, just scaffold the exact same assembly twice instead of correcting the assembly for one of the runs. Or you can correct the assembly and then use those corrected sequences for both scaffolding runs.

As for the second error message:

RuntimeError: There are no useful alignments. Check output alignment files

Please open up a separate issue and we can debug from there. One thing to try first is deleting the output directory or using -w.

[ysawires12345678]

Hello, I figured what was wrong with my commands. I reached to the level of having up to 5 .agp files. I validate them with the on line NCBI validation tool and corrected manually the columns numbers (but I get the message "all objects are singletons with component_beg=1" from the online validation tool). when I run merge I still get the "ValueError: Input AGPs do not have the same set of components". I will try to email 3 of the .agp file; if you would kindly be able to help with this?

[malonge]

sure you can email me at [email protected]. I can take a look at the AGP files and see what is going on.

[xiekunwhy]

Hi,

I got the same errors, and two agp files are attached, would you please take a look at?

agpfile.zip

Best, Kun

[malonge]

@xiekunwhy I checked your AGP files and I could not find anything obviously wrong. Do you mind opening up a separate issue? Please provide the following aside from the AGP files you aready provided (you can also email me).

• The assembly
• the exact command
• the exact error message

Sorry about the inconvenience

[wjq1981]

Hi,

I got the same errors, and two agp files are attached, would you please take a look at?

agpfile.zip

Best, Kun

Hi, did you get your problem solved? I am having the same problem, but trying to modify it did not help.

[liuyu988]

Hi there,

So I will first comment on the original error: ValueError: Input AGPs do not have the same set of components

In order to use merge, the AGPs file must contain the same set of components. In other words, the AGP files must be ordering and orienting the exact same set of sequences. So to address this, just scaffold the exact same assembly twice instead of correcting the assembly for one of the runs. Or you can correct the assembly and then use those corrected sequences for both scaffolding runs.

As for the second error message:

RuntimeError: There are no useful alignments. Check output alignment files

Please open up a separate issue and we can debug from there. One thing to try first is deleting the output directory or using -w.

Hi , i met the same problem, and I solved this by using -w, but i did't make sense why. Could you offer some help for me? thanks a lot! Yu

[mwylerCH]

Hi there, So I will first comment on the original error: ValueError: Input AGPs do not have the same set of components In order to use merge, the AGPs file must contain the same set of components. In other words, the AGP files must be ordering and orienting the exact same set of sequences. So to address this, just scaffold the exact same assembly twice instead of correcting the assembly for one of the runs. Or you can correct the assembly and then use those corrected sequences for both scaffolding runs. As for the second error message: RuntimeError: There are no useful alignments. Check output alignment files Please open up a separate issue and we can debug from there. One thing to try first is deleting the output directory or using -w.

Hi , i met the same problem, and I solved this by using -w, but i did't make sense why. Could you offer some help for me? thanks a lot! Yu

RagTag uses files that he produced previously. Therefor by using -wthey will be removed and you will exclude the chance of an error from a previous wrong run.