search

rnajena / poseidon

PoSeiDon: positive selection detection and recombination analysis pipeline
MIT License
35 stars 10 forks source link

Process killed at FASTA format check, no error msg #25

Closed DrPintoThe2nd closed 3 years ago

DrPintoThe2nd commented 3 years ago

Dear Poseidon team,

I am at a loss, I have subset the data and changed names, etc. The pipeline quits without an error..

[Running 48 thread Ubuntu 16.04 w/ 128Gb RAM.. should be no issues there.]

The only thing I can think of is the translation scheme is non-standard.. comments, suggestions, help?

"" bjp$ nextflow run hoelzer/poseidon -r v1.0.1 --fasta ~/poseidon/test_data/seq.fasta -profile local,docker N E X T F L O W ~ version 20.10.0 Launching hoelzer/poseidon [intergalactic_mirzakhani] - revision: 4f23bb667f [v1.0.1] WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE

P O S E I D O N

Profile: local,docker

Current User: bjp Nextflow-version: 20.10.0 Starting time: 01-11-2020 15:14 UTC Workdir location: /tmp/nextflow-work-bjp

CPUs to use per process: 6, maximal CPUs to use: 48

Tree root species: NA Reference species: NA

Use KH-insignificant breakpoints: no

[- ] process > check_fasta_format - [- ] process > translatorx - [- ] process > check_aln - [- ] process > remove_gaps - [- ] process > raxml_nt - [- ] process > raxml_aa - executor > local (1) [4a/8e9e14] process > check_fasta_format (1) [ 0%] 0 of 1 [- ] process > translatorx - [- ] process > check_aln - [- ] process > remove_gaps - [- ] process > raxml_nt - [- ] process > raxml_aa - executor > local (1) [4a/8e9e14] process > check_fasta_format (1) [ 0%] 0 of 1 [- ] process > translatorx - [- ] process > check_aln - [- ] process > remove_gaps - [- ] process > raxml_nt - [- ] process > raxml_aa - [- ] process > raxml2drawing - bjp:~/poseidon$ - [<------------and it does this?] [- ] process > barefoot - [- ] process > model_selection - [- ] process > gard_detect - [- ] process > gard_process - [- ] process > codeml_built - [- ] process > codeml_run - [- ] process > codeml_combine - [- ] process > tex_built - [- ] process > pdflatex_single - [- ] process > build_fragments - [- ] process > frag_raxml_nt - [- ] process > frag_raxml_aa - [- ] process > frag_raxml2drawing - [- ] process > frag_nw_display - [- ] process > frag_barefoot - [- ] process > frag_codeml_built - [- ] process > frag_codeml_run - [- ] process > frag_codeml_combine - [- ] process > frag_tex_built - [- ] process > frag_pdflatex_single - [- ] process > tex_combine - [- ] process > pdflatex_full - [- ] process > frag_aln_html - [- ] process > html_frag - [- ] process > frag_publish - [- ] process > frag_html_codeml - [- ] process > html - [- ] process > html_codeml - [- ] process > html_params - [- ] process > html_recomb - "" Thanks so much! Best, bjp

hoelzer commented 3 years ago

Hi @DrPintoThe2nd !

Thanks for your interest in using PoSeiDon!

Can you check the files in the folder 

ls -lah /tmp/nextflow-work-bjp/4a/8e9e14]*/

?

There should be a .command.log that might give us some more insight into what's going on.

Does your FASTA file contain protein-coding homologous sequences?

DrPintoThe2nd commented 3 years ago

Hi Martin,

Thanks for your timely response. I've been pulled away on some other projects and my collaborator has decided to try and work through the issue. I'll close for now and re-open if I have some time to continue troubleshooting.

Thanks again, bjp