You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
$SCAF2BIN and $SCAF2BINIDs are variables listing the input directories (n=3; comma-delim) and binner IDs, respectively.
The output:
User environment details:
Rscript path: /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb228
41d8103fa9/bin/Rscript
Rscript version: R scripting front-end version 4.0.3 (2020-10-10)
pullseq path: /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb228
41d8103fa9/bin/pullseq
pullseq version: Version: 1.0.2 Name lookup method: UTHASH
prodigal path: /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22
841d8103fa9/bin/prodigal
prodigal version: Prodigal V2.6.3: February, 2016
ruby path: /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d
8103fa9/bin/ruby
ruby version: ruby 3.1.0p0 (2021-12-25 revision fb4df44d16) [x86_64-linux]
diamond path: /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb228
41d8103fa9/bin/diamond
diamond version: diamond version 0.9.36
Running DAS Tool using 8 threads.
predicting genes using Prodigal V2.6.3: February, 2016
identifying single copy genes using diamond version 2.0.14
/tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:793:in `flock': Bad file descriptor @ rb_file_flock - /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/gems/3.1.0/specifications/default/abbrev-0.1.0.gemspec (Errno::EBADF)
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:793:in `block in open_with_flock'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:790:in `open'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:790:in `open_with_flock'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:1119:in `load'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:800:in `block in each_spec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:772:in `block (2 levels) in each_gemspec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:771:in `each'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:771:in `block in each_gemspec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:770:in `each'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:770:in `each_gemspec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:799:in `each_spec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:870:in `load_defaults'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:1353:in `<top (required)>'
from <internal:gem_prelude>:2:in `require'
from <internal:gem_prelude>:2:in `<internal:gem_prelude>'
mv: cannot stat '/ebio/abt3_projects/databases_no-backup/DeepMAsED/version2/real_data_eval/UHGG/LLMGQC_r100/LLMGA/bin_refine/ERS235591/DAS_Tool/bins_proteins.faa.scg': No such file or directory
/tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:793:in `flock': Bad file descriptor @ rb_file_flock - /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/gems/3.1.0/specifications/default/abbrev-0.1.0.gemspec (Errno::EBADF)
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:793:in `block in open_with_flock'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:790:in `open'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:790:in `open_with_flock'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:1119:in `load'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:800:in `block in each_spec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:772:in `block (2 levels) in each_gemspec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:771:in `each'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:771:in `block in each_gemspec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:770:in `each'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:770:in `each_gemspec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:799:in `each_spec'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems/specification.rb:870:in `load_defaults'
from /tmp/global2/nyoungblut/code/dev/ll_pipelines/llmga/.snakemake/conda/1e05d32c9539bd805bb22841d8103fa9/lib/ruby/3.1.0/rubygems.rb:1353:in `<top (required)>'
from <internal:gem_prelude>:2:in `require'
from <internal:gem_prelude>:2:in `<internal:gem_prelude>'
mv: cannot stat '/ebio/abt3_projects/databases_no-backup/DeepMAsED/version2/real_data_eval/UHGG/LLMGQC_r100/LLMGA/bin_refine/ERS235591/DAS_Tool/bins_proteins.faa.scg': No such file or directory
rm: cannot remove '/ebio/abt3_projects/databases_no-backup/DeepMAsED/version2/real_data_eval/UHGG/LLMGQC_r100/LLMGA/bin_refine/ERS235591/DAS_Tool/bins_proteins.faa.findSCG.b6': No such file or directory
rm: cannot remove '/ebio/abt3_projects/databases_no-backup/DeepMAsED/version2/real_data_eval/UHGG/LLMGQC_r100/LLMGA/bin_refine/ERS235591/DAS_Tool/bins_proteins.faa.scg.candidates.faa': No such file or directory
rm: cannot remove '/ebio/abt3_projects/databases_no-backup/DeepMAsED/version2/real_data_eval/UHGG/LLMGQC_r100/LLMGA/bin_refine/ERS235591/DAS_Tool/bins_proteins.faa.all.b6': No such file or directory
single copy gene prediction using diamond failed. Aborting
I'm using
bioconda::das_tool=1.1.3
with the following command:$SCAF2BIN
and$SCAF2BINIDs
are variables listing the input directories (n=3; comma-delim) and binner IDs, respectively.The output:
My conda env:
The text was updated successfully, but these errors were encountered: