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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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Creating empty mblocks file #124

Open lkavan2 opened 1 year ago

lkavan2 commented 1 year ago

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 commented 1 year ago

Thanks for opening an issue! Could you

With those, I hopefully can help debug this issue.

lkavan2 commented 1 year ago

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 Profilehttp://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

With those, I hopefully can help debug this issue.

— Reply to this email directly, view it on GitHubhttps://github.com/marbl/parsnp/issues/124#issuecomment-1650489931, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7KPBOV6UYPDOFRJAKGJTDLXSASKDANCNFSM6AAAAAAXF3DAPY. You are receiving this because you authored the thread.Message ID: @.***>

bkille commented 1 year ago

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 commented 1 year ago

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 Profilehttp://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 GitHubhttps://github.com/marbl/parsnp/issues/124#issuecomment-1652529647, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7KPBOQBZWMHWT6CJRMZDN3XSGEVLANCNFSM6AAAAAAXF3DAPY. You are receiving this because you authored the thread.Message ID: @.***>

bkille commented 1 year ago

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 commented 1 year ago

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 Profilehttp://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 GitHubhttps://github.com/marbl/parsnp/issues/124#issuecomment-1655721055, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7KPBOQFK7WMKRH2XH6FKCLXSO7RZANCNFSM6AAAAAAXF3DAPY. You are receiving this because you authored the thread.Message ID: @.***>