Error on Roary to Plink

[adriangeerre]

Hi @francesccoll

Thanks for a nice tool. I have been looking for something like this for some time.

I am trying to run the tool (using nextflow and Docker/Singularity) on a clade of 39 bacterias grouped by Genus. There might be a few species but the strains have a mean similarity of approx. 90% (FastANI). Is your tool suited for that purpose?

To run the pipeline I am using a phylogeny created by Mashtree and a pangenome made by Roary. Below are the execution code and the error log. Could you provide some guidance?

Thank you for the help.

Best regards,
Adrián

Execution

nextflow run nextflow/main.nf --tree btstrp.MesorhizobiumSubset_c1.distmat --pangenome gene_presence_absence.Mesorhizobium_subset.Rtab --outprefix MesoSubset --run_prepare_pangenome --results_dir PwBacGWAS --num_cores 2

Log:

N E X T F L O W  ~  version 20.10.0
Launching `nextflow/main.nf` [infallible_church] - revision: 76eb19d0f2
2 cores will be used for multiprocessing tasks
executor >  local (2)
[56/c4d374] process > PREPARE_PG:roary_to_plink_files (1)  [  0%] 0 of 1
[95/8b3231] process > PREPARE_PG:roary_to_pastml_matrix... [100%] 1 of 1 ✔
Error executing process > 'PREPARE_PG:roary_to_plink_files (1)'

Caused by:
  Missing output file(s) `MesoSubset.bed` expected by process `PREPARE_PG:roary_to_plink_files (1)`

Command executed:

  roary_to_plink_files.py --gene_presence_absence "gene_presence_absence.Mesorhizobium_subset.Rtab" --input_format 2 --output_prefix "MesoSubset"

Command exit status:
  0

Command output:
  --vcf: 15k variants complete.
  --vcf: 16k variants complete.
  --vcf: 17k variants complete.
  --vcf: 18k variants complete.
  --vcf: 19k variants complete.
  --vcf: 20k variants complete.
  --vcf: 21k variants complete.
  --vcf: 22k variants complete.
  --vcf: 23k variants complete.
  --vcf: 24k variants complete.
  --vcf: 25k variants complete.
  --vcf: 26k variants complete.
  --vcf: 27k variants complete.
  --vcf: 28k variants complete.
  --vcf: 29k variants complete.
  --vcf: 30k variants complete.
  --vcf: 31k variants complete.
  --vcf: 32k variants complete.
  --vcf: 33k variants complete.
  --vcf: 34k variants complete.
  --vcf: 35k variants complete.
  --vcf: 36k variants complete.
  --vcf: 37k variants complete.
  --vcf: 38k variants complete.
  --vcf: 39k variants complete.
  --vcf: 40k variants complete.
  --vcf: 41k variants complete.
  --vcf: 42k variants complete.
  --vcf: 43k variants complete.
  --vcf: 44k variants complete.
  --vcf: 45k variants complete.
  --vcf: 46k variants complete.
  --vcf: 47k variants complete.
  --vcf: 48k variants complete.
  --vcf: 49k variants complete.
  --vcf: 50k variants complete.
  --vcf: 51k variants complete.
  --vcf: 52k variants complete.
executor >  local (2)
[56/c4d374] process > PREPARE_PG:roary_to_plink_files (1)  [100%] 1 of 1, failed: 1 ✘
[95/8b3231] process > PREPARE_PG:roary_to_pastml_matrix... [100%] 1 of 1 ✔
Error executing process > 'PREPARE_PG:roary_to_plink_files (1)'

Caused by:
  Missing output file(s) `MesoSubset.bed` expected by process `PREPARE_PG:roary_to_plink_files (1)`

Command executed:

  roary_to_plink_files.py --gene_presence_absence "gene_presence_absence.Mesorhizobium_subset.Rtab" --input_format 2 --output_prefix "MesoSubset"

Command exit status:
  0

Command output:
  --vcf: 15k variants complete.
  --vcf: 16k variants complete.
  --vcf: 17k variants complete.
  --vcf: 18k variants complete.
  --vcf: 19k variants complete.
  --vcf: 20k variants complete.
  --vcf: 21k variants complete.
  --vcf: 22k variants complete.
  --vcf: 23k variants complete.
  --vcf: 24k variants complete.
  --vcf: 25k variants complete.
  --vcf: 26k variants complete.
  --vcf: 27k variants complete.
  --vcf: 28k variants complete.
  --vcf: 29k variants complete.
  --vcf: 30k variants complete.
  --vcf: 31k variants complete.
  --vcf: 32k variants complete.
  --vcf: 33k variants complete.
  --vcf: 34k variants complete.
  --vcf: 35k variants complete.
  --vcf: 36k variants complete.
  --vcf: 37k variants complete.
  --vcf: 38k variants complete.
  --vcf: 39k variants complete.
  --vcf: 40k variants complete.
  --vcf: 41k variants complete.
  --vcf: 42k variants complete.
  --vcf: 43k variants complete.
  --vcf: 44k variants complete.
  --vcf: 45k variants complete.
  --vcf: 46k variants complete.
  --vcf: 47k variants complete.
  --vcf: 48k variants complete.
  --vcf: 49k variants complete.
  --vcf: 50k variants complete.
  --vcf: 51k variants complete.
  --vcf: 52k variants complete.
  --vcf: 53k variants complete.
  --vcf: 54k variants complete.
  --vcf: 55k variants complete.
  --vcf: 56k variants complete.
  --vcf: 57k variants complete.
  --vcf: 58k variants complete.
  --vcf: MesoSubset-temporary.bed + MesoSubset-temporary.bim +
  MesoSubset-temporary.fam written.
  Number of samples: 39. Number of variants: 58413
  Running
  plink --vcf MesoSubset_tmp.vcf --make-bed --double-id --out MesoSubset
  ERROR: Command 'plink --vcf MesoSubset_tmp.vcf --make-bed --double-id --out MesoSubset' returned non-zero exit status 3.

Command error:
  2023-05-10 09:32:41,452 INFO: Making sure dependencies exist...
  2023-05-10 09:32:41,458 INFO: plink is installed!
  2023-05-10 09:32:41,458 INFO: Making sure input files exist...
  2023-05-10 09:32:41,458 INFO: Reading Roary file gene_presence_absence.Mesorhizobium_subset.Rtab...
  2023-05-10 09:32:41,690 INFO: Reading Roary file gene_presence_absence.Mesorhizobium_subset.Rtab. DONE
  2023-05-10 09:32:41,690 INFO: Converting Roary file gene_presence_absence.Mesorhizobium_subset.Rtab into intermediate VCF...
  2023-05-10 09:32:46,228 INFO: Converting Roary file gene_presence_absence.Mesorhizobium_subset.Rtab into intermediate VCF. DONE.
  2023-05-10 09:32:46,228 INFO: Running PLINK to convert intermediate VCF file to BED format...
  Error: Invalid centimorgan position on line 1765 of .bim file.
  2023-05-10 09:32:46,319 INFO: Running PLINK to convert intermediate VCF file to BED format. DONE.

Work dir:
  04-GWAS/Mesorhizobium/work/56/c4d374495d2f235fdfdb34d8acabb8

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`