Dear Pasi,
I just started using Lep-MAP3 (v. 0.5) for linkage map construction for F2 self-crossed tomato population.
ParentCall2 successfully read my data and saved the data for next stage. I did not use the "removeNonInformative=1" options when running ParentCall2.
Here is the ParentCall2command I used: java -cp .\bin\ ParentCall2 data=tomato_F2_pedigree.txt vcfFile=format_2_final_for_mapping.vcf >t_data_p.call
However, I encountered Error:504 when running Filtering2 with "dataTolerance=NUM" and "removeNonInformative=1" option. I have attached screenshots of the error message, Filtering2 command, ParentCall2 output data, and my TASSEL-generated VCF file for your reference.
Could you please help me fix the issue based on this information?
I greatly appreciate in advance for your time and assistance.
Best Regards,
Farid
Thank you for your question and sorry to hear you about your problem with Lep-MAP3.
I cannot find anything wrong in your commands, they seem ok. The error message is originating from the part where the data is read and the marker name is extracted. Lep-MAP3 does not find two tab separated fields from the line.
I cannot say exactly what the problem is. Maybe it is the end of line characters (\r\n) in dos? I know that some windows text editors can fix/change these (I haven't used windows for over 20 years, sorry). Check also that the error stream is not mixed with the output, adding something like "... 2>err.txt" to ParentCall2 command might be safer.
If you can find a minimal input where Filtering2 fails (e.g. first 10 lines) and share this with me, I can figure out more.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-05-13
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Dear Pasi,
Thanks for your reply!
You were right about the end-of-line issue. I ran the same command and data in the Linux environment within Windows (WSL2), and it worked successfully.
Out of curiosity, like I mentioned earlier, ParentCall2 was able to read my data and generate a "CALL File." However, Filtering2 couldn't read this same "CALL File." This makes it seem like ParentCall2 might not be creating a correct "CALL File." Interestingly, in the Linux system, Filtering2 had no problem reading the "CALL File" generated by ParentCall2. This strange behavior is quite confusing.
Anyway, thank you again for developing such a wonderful tool.
Best Regards,
Farid
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Thanks for noting this. I will try to test the software in windows as well.
This might also help: you can (maybe) add -Dline.separator=$'\n' to java command to set the end of line separator to \n. Or to -Dline.separator=$'\r\n' if it then works.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi,
I just started using Lep-MAP3 (v. 0.5) for linkage map construction for F2 self-crossed tomato population.
ParentCall2 successfully read my data and saved the data for next stage. I did not use the "removeNonInformative=1" options when running ParentCall2.
Here is the ParentCall2command I used:
java -cp .\bin\ ParentCall2 data=tomato_F2_pedigree.txt vcfFile=format_2_final_for_mapping.vcf >t_data_p.call
However, I encountered Error:504 when running Filtering2 with "dataTolerance=NUM" and "removeNonInformative=1" option. I have attached screenshots of the error message, Filtering2 command, ParentCall2 output data, and my TASSEL-generated VCF file for your reference.
Could you please help me fix the issue based on this information?
I greatly appreciate in advance for your time and assistance.
Best Regards,
Farid
Dear Farid,
Thank you for your question and sorry to hear you about your problem with Lep-MAP3.
I cannot find anything wrong in your commands, they seem ok. The error message is originating from the part where the data is read and the marker name is extracted. Lep-MAP3 does not find two tab separated fields from the line.
I cannot say exactly what the problem is. Maybe it is the end of line characters (\r\n) in dos? I know that some windows text editors can fix/change these (I haven't used windows for over 20 years, sorry). Check also that the error stream is not mixed with the output, adding something like "... 2>err.txt" to ParentCall2 command might be safer.
If you can find a minimal input where Filtering2 fails (e.g. first 10 lines) and share this with me, I can figure out more.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-05-13
Dear Pasi,
Thanks for your reply!
You were right about the end-of-line issue. I ran the same command and data in the Linux environment within Windows (WSL2), and it worked successfully.
Out of curiosity, like I mentioned earlier, ParentCall2 was able to read my data and generate a "CALL File." However, Filtering2 couldn't read this same "CALL File." This makes it seem like ParentCall2 might not be creating a correct "CALL File." Interestingly, in the Linux system, Filtering2 had no problem reading the "CALL File" generated by ParentCall2. This strange behavior is quite confusing.
Anyway, thank you again for developing such a wonderful tool.
Best Regards,
Farid
Dear Farid,
Thanks for noting this. I will try to test the software in windows as well.
This might also help: you can (maybe) add -Dline.separator=$'\n' to java command to set the end of line separator to \n. Or to -Dline.separator=$'\r\n' if it then works.
Cheers,
Pasi