Run stops after successful check_input #83
Description
Hello,
Working with fastoma v0.3.4 for a while now, i wanted to give a try to the latest version, but i encountered an issue.
I pulled the latest release, created a conda with the given yml, and used the same proteomes i used for the v0.3.4.
My problem is that the runs stops after successfully check my inputs :
`
N E X T F L O W ~ version 25.10.2
Launching path/fastoma0.5.1/FastOMA/FastOMA.nf [extravagant_mayer] DSL2 - revision: a37f924c02
Input options
input : pathdata/fastoma0.5.1/on_10_species/input/
omamer_db : path/scripts/all_FastOMA/FastOMA/LUCA.h5
Output options
output_folder : path/data/fastoma0.5.1/on_10_species
hogmap_folder : path/data/fastoma0.5.1/on_10_species/hogmap
Output control
msa_folder : path/data/fastoma0.5.1/on_10_species/msa
temp_output : path/data/fastoma0.5.1/on_10_species/temp_output
genetrees_folder : path/data/fastoma0.5.1/on_10_species/genetrees
Resource options
time_multiplier : 4
memory_multiplier : 4
Generic options
report : true
statsdir : path/data/fastoma0.5.1/on_10_species/stats
trace_report_suffix: 2026-01-16_11-51-33
Core Nextflow options
runName : extravagant_mayer
launchDir : path/data/fastoma0.5.1/on_10_species
workDir : path/data/fastoma0.5.1/on_10_species/work
projectDir : path/scripts/all_FastOMA/fastoma0.5.1/FastOMA
userName : lalam
profile : large
configFiles : path/scripts/all_FastOMA/fastoma0.5.1/FastOMA/nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
[- ] check_input -
[- ] omamer_run -
[- ] infer_roothogs -
[- ] batch_roothogs -
[- ] check_input | 0 of 1
[- ] omamer_run -
[- ] infer_roothogs -
[- ] batch_roothogs -
[- ] hog_big -
[- ] hog_rest -
[- ] collect_subhogs -
[- ] ext…airwise_ortholog_relations -
[- ] fastoma_report -
executor > local (1)
[85/b1ddd0] check_input (1) | 0 of 1
[- ] omamer_run -
[- ] infer_roothogs -
[- ] batch_roothogs -
[- ] hog_big -
[- ] hog_rest -
[- ] collect_subhogs -
[- ] ext…airwise_ortholog_relations -
[- ] fastoma_report -
executor > local (1)
[85/b1ddd0] check_input (1) | 1 of 1 ✔
[- ] omamer_run -
[- ] infer_roothogs -
[- ] batch_roothogs -
[- ] hog_big -
[- ] hog_rest -
[- ] collect_subhogs -
[- ] ext…airwise_ortholog_relations -
[- ] fastoma_report -
Completed at : 2026-01-16T11:51:48.609273916+01:00
Duration : 13.5s
Processes : 1 (success), 0 (failed)
Output in : path/data/fastoma0.5.1/on_10_species
Nextflow report : path/data/fastoma0.5.1/on_10_species/stats
Done!
`
Here is my log for inputs checking:
`
2026-01-16 11:51:40,118 DEBUG FastOMA: Arguments: Namespace(proteomes='proteome', species_tree='species_tree.nwk', out_tree='species_tree_checked.nwk', splice='splice', hogmap='hogmap_in', omamer_db='LUCA.h5', v=2)
2026-01-16 11:51:40,120 INFO FastOMA: There are 10 files in the proteome folder.
2026-01-16 11:51:40,123 INFO FastOMA: The species tree has 10 leaves.
2026-01-16 11:51:40,123 INFO FastOMA: The species tree has 10 leaves
2026-01-16 11:51:40,124 INFO FastOMA: After pruning, the species tree has 10 leaves
2026-01-16 11:51:40,126 DEBUG FastOMA: The new species tree is written species_tree_checked.nwk
2026-01-16 11:51:40,127 DEBUG FastOMA: using 'proteome' as proteome folder, found 10 files
2026-01-16 11:51:40,127 DEBUG FastOMA: Drosophila.melanogaster.fasta: Drosophila.melanogaster | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Xenopus.tropicalis.fasta: Xenopus.tropicalis | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Gallus.gallus.fasta: Gallus.gallus | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Monodelphis.domestica.fasta: Monodelphis.domestica | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Mus.musculus.fasta: Mus.musculus | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Lepisosteus.oculatus.fasta: Lepisosteus.oculatus | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Danio.rerio.fasta: Danio.rerio | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Gasterosteus.aculeatus.fasta: Gasterosteus.aculeatus | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Salmo.salar.fasta: Salmo.salar | fasta
2026-01-16 11:51:40,127 DEBUG FastOMA: Homo.sapiens.fasta: Homo.sapiens | fasta
2026-01-16 11:51:40,325 INFO FastOMA: Danio.rerio contains 24983 that are at least 0 long.
2026-01-16 11:51:40,379 INFO FastOMA: Drosophila.melanogaster contains 10126 that are at least 0 long.
2026-01-16 11:51:40,524 INFO FastOMA: Gallus.gallus contains 16811 that are at least 0 long.
2026-01-16 11:51:40,692 INFO FastOMA: Gasterosteus.aculeatus contains 19905 that are at least 0 long.
2026-01-16 11:51:40,893 INFO FastOMA: Homo.sapiens contains 19640 that are at least 0 long.
2026-01-16 11:51:40,997 INFO FastOMA: Lepisosteus.oculatus contains 18110 that are at least 0 long.
2026-01-16 11:51:41,209 INFO FastOMA: Monodelphis.domestica contains 21229 that are at least 0 long.
2026-01-16 11:51:41,449 INFO FastOMA: Mus.musculus contains 21908 that are at least 0 long.
2026-01-16 11:51:41,842 INFO FastOMA: Salmo.salar contains 46854 that are at least 0 long.
2026-01-16 11:51:41,958 INFO FastOMA: Xenopus.tropicalis contains 21780 that are at least 0 long.
2026-01-16 11:51:41,958 INFO FastOMA: There are 10 species in the proteome folder.
2026-01-16 11:51:48,203 INFO FastOMA: There are 221346 proteins in total in the input proteome folder.
2026-01-16 11:51:48,205 INFO FastOMA: OMAmer db or hogmap exist. It looks ok.
2026-01-16 11:51:48,205 INFO FastOMA: Splice folder doesn't exist and that's ok.
2026-01-16 11:51:48,205 INFO FastOMA: Input check finished successfully (since no error is found)!`
the number of proteins found is the one expected. The only modification i did is to change --input_folder into --input, as mentionned.