marbl/parsnp

Creating empty mblocks file

lkavan2 opened this issue · 6 comments

lkavan2 commented

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

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 commented
bkille commented

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
bkille commented

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