Creating empty mblocks file

[lkavan2]

Hello. Currently running mac and downloaded harvesttools using conda.

When I run normal parsnp command, I get the following error:
base) > ~ % parsnp -g ~/GCF_PAO1_000006765.1_ASM676v1_genomic.gbff -d ~/WR_fna -p 3 -c
11:30:52 - INFO - |--Parsnp 1.7.4--|

Ref ~/tmp/GCF_PAO1_000006765.1_ASM676v1_genomic.gbff.fna
11:35:06 - INFO -

---

SETTINGS:
|-refgenome: //GCF_PAO1_000006765.1_ASM676v1_genomic.gbff
|-genomes:
/ncbi-genomes-2022-08-31/WR_fna/GCF_003968125.1_ASM396812v1_genomic.fna
//GCF_003968155.1_ASM396815v1_genomic.fna
...96 more file(s)...
//GCF_003970625.1_ASM397062v1_genomic.fna
//GCF_003977965.1_ASM397796v1_genomic.fna
|-aligner: muscle
|-outdir: //P_2023_04_20_113052300077
|-OS: Darwin
|-threads: 3

---

11:35:06 - INFO - <>
11:35:17 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner...
12:12:13 - INFO - Reconstructing core genome phylogeny...
12:12:14 - CRITICAL - The following command failed:
>>$ raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T 3 -s /~/tmpkuao1ae0 -n OUTPUT
Please veryify input data and restart Parsnp.
If the problem persists please contact the Parsnp development team.

  STDOUT:
  Warning, you specified a working directory via "-w"

Keep in mind that RAxML only accepts absolute path names, not relative ones!

RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file

TOO FEW SPECIES

  STDERR:

So I tried to use FastTrees and ended with this error:

~ % parsnp -c -g ~/GCF_PAO1_000006765.1_ASM676v1_genomic.gbff -d //WR_fna -p 3 -u --use-fasttree
12:21:22 - INFO - |--Parsnp 1.7.4--|

12:25:33 - INFO - <>
12:25:40 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner...
13:01:05 - INFO - Reconstructing core genome phylogeny...
13:01:05 - CRITICAL - The following command failed:
>>$ FastTreeMP -nt -quote -gamma -slow -boot 100 //P_2023_04_20_122122352256/parsnp.snps.mblocks > //P_2023_04_20_122122352256/parsnp.tree
Please veryify input data and restart Parsnp.
If the problem persists please contact the Parsnp development team.

  STDOUT:

In both cases I end with an empty mblocks file. Can someone help me?

[bkille]

Thanks for opening an issue! Could you

• Provide the output of the command with the --verbose flag
• Provide the contents of the parsnpAligner.log file

With those, I hopefully can help debug this issue.

[lkavan2]

Thank you for reaching out! I was able to solve the problem of the empty mblocks file. However, I was never able to figure out why I had such large gaps in the Ginger viewer ( see attached). I checked to make sure that my sequences were highly similar using ANI (all 100 sequences were ~96-100% similar). Also, the regions missing were annotated in each of the genomes gbff files. Any advice would be great! Thank you again, Logan Kavanaugh, MSc. Pronouns: She/Her/Hers

…

_____________________________________________ PhD Candidate | Microbiology and Molecular Genetics Program Conn Lab | Department of Biochemistry | Emory University LinkedIn Profile<http://www.linkedin.com/in/logan-kavanaugh-m-sc-489b27180> From: Bryce Kille ***@***.***> Date: Tuesday, July 25, 2023 at 4:14 PM To: marbl/parsnp ***@***.***> Cc: Kavanaugh, Logan ***@***.***>, Author ***@***.***> Subject: [External] Re: [marbl/parsnp] Creating empty mblocks file (Issue #124) Thanks for opening an issue! Could you * Provide the output of the command with the --verbose flag * Provide the contents of the parsnpAligner.log file With those, I hopefully can help debug this issue. — Reply to this email directly, view it on GitHub<#124 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7KPBOV6UYPDOFRJAKGJTDLXSASKDANCNFSM6AAAAAAXF3DAPY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[bkille]

Does the reference and/or any of the inputs have multiple contigs? Unfortunately, I don't work on the Gingr repo, but I do know that the header information of multi-contig inputs in the parsnp.xmfa output can give Gingr trouble occasionally ):

[lkavan2]

Oh no! That probably is it. Any chance you can put me in touch with a Gingr repo that might be able to help? Thank you so much, Logan Kavanaugh, MSc. Pronouns: She/Her/Hers

…

_____________________________________________ PhD Candidate | Microbiology and Molecular Genetics Program Conn Lab | Department of Biochemistry | Emory University LinkedIn Profile<http://www.linkedin.com/in/logan-kavanaugh-m-sc-489b27180> From: Bryce Kille ***@***.***> Date: Wednesday, July 26, 2023 at 5:36 PM To: marbl/parsnp ***@***.***> Cc: Kavanaugh, Logan ***@***.***>, Author ***@***.***> Subject: [External] Re: [marbl/parsnp] Creating empty mblocks file (Issue #124) Does the reference and/or any of the inputs have multiple contigs? Unfortunately, I don't work on the Gingr repo, but I do know that the header information of multi-contig inputs in the parsnp.xmfa output can give Gingr trouble occasionally ): — Reply to this email directly, view it on GitHub<#124 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7KPBOQBZWMHWT6CJRMZDN3XSGEVLANCNFSM6AAAAAAXF3DAPY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[bkille]

Hmm, I'm not sure who maintains that repository now. Would you mind pasting the output of the parsnpAligner.ini file here? If parsnp truly isn't aligning that region, then it should be a parsnp issue. otherwise, it will be a gingr issue.

[lkavan2]

Sure! Thanks for your help. Logan Kavanaugh, MSc. Pronouns: She/Her/Hers

…

_____________________________________________ PhD Candidate | Microbiology and Molecular Genetics Program Conn Lab | Department of Biochemistry | Emory University LinkedIn Profile<http://www.linkedin.com/in/logan-kavanaugh-m-sc-489b27180> From: Bryce Kille ***@***.***> Date: Friday, July 28, 2023 at 9:50 AM To: marbl/parsnp ***@***.***> Cc: Kavanaugh, Logan ***@***.***>, Author ***@***.***> Subject: [External] Re: [marbl/parsnp] Creating empty mblocks file (Issue #124) Hmm, I'm not sure who maintains that repository now. Would you mind pasting the output of the parsnpAligner.ini file here? If parsnp truly isn't aligning that region, then it should be a parsnp issue. otherwise, it will be a gingr issue. — Reply to this email directly, view it on GitHub<#124 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7KPBOQFK7WMKRH2XH6FKCLXSO7RZANCNFSM6AAAAAAXF3DAPY>. You are receiving this because you authored the thread.Message ID: ***@***.***>