I am using finishM 0.0.9, and I got error messages below.
I have tested comand I use successully with small fastq files, is this because of not enough cpus or too much input data? Do you have suggestions about this error message?
/ruby/2.7.1/lib/ruby/gems/2.7.0/gems/bio-commandeer-0.4.0/lib/bio-commandeer/commandeer.rb:62:in `raise_if_failed': Command returned non-zero exit status (42), likely indicating failure. Command run was clustalo -t DNA -i - --output-order=input-order and the STDERR was: (Bio::CommandFailedException)
STDOUT was:
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/bio-commandeer-0.4.0/lib/bio-commandeer/commandeer.rb:17:in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/assembly/contig_printer.rb:324:inclustalo'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/assembly/contig_printer.rb:179:in sequences_to_variants_conservative' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/assembly/contig_printer.rb:107:inready_two_contigs_and_connections'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:197:in block (6 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:175:ineach'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:175:in each_with_index' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:175:inblock (5 levels) in run'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:164:in each' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:164:ineach_with_index'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:164:in block (4 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:159:inopen'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:159:in block (3 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:158:inopen'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:158:in block (2 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:136:inopen'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:136:in block in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:129:ineach'
from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:129:in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/bin/finishm:138:in<top (required)>'
from /ruby/2.7.1/bin/finishm:23:in load' from /ruby/2.7.1/bin/finishm:23:in'
Hi,
I am using finishM 0.0.9, and I got error messages below.
I have tested comand I use successully with small fastq files, is this because of not enough cpus or too much input data? Do you have suggestions about this error message?
/ruby/2.7.1/lib/ruby/gems/2.7.0/gems/bio-commandeer-0.4.0/lib/bio-commandeer/commandeer.rb:62:in `raise_if_failed': Command returned non-zero exit status (42), likely indicating failure. Command run was clustalo -t DNA -i - --output-order=input-order and the STDERR was: (Bio::CommandFailedException)
STDOUT was: from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/bio-commandeer-0.4.0/lib/bio-commandeer/commandeer.rb:17:in'
run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/assembly/contig_printer.rb:324:inclustalo' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/assembly/contig_printer.rb:179:insequences_to_variants_conservative' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/assembly/contig_printer.rb:107:inready_two_contigs_and_connections' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:197:inblock (6 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:175:ineach' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:175:ineach_with_index' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:175:inblock (5 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:164:ineach' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:164:ineach_with_index' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:164:inblock (4 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:159:inopen' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:159:inblock (3 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:158:inopen' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:158:inblock (2 levels) in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:136:inopen' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:136:inblock in run' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:129:ineach' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/lib/finishm/roundup.rb:129:inrun' from /ruby/2.7.1/lib/ruby/gems/2.7.0/gems/finishm-0.0.9/bin/finishm:138:in<top (required)>' from /ruby/2.7.1/bin/finishm:23:inload' from /ruby/2.7.1/bin/finishm:23:inThanks, Jie