transfuse --assemblies assembly1,assembly2 --left left_reads --right right_reads -output output_file --threads 6
[ERROR] 2016-02-05 05:42:30 : Version Info: A newer version of Salmon with important new features is availaible;
--output merged.fa
--output
parameter was a PATH file
https://github.com/cboursnell/transfuse/releases
yes?
bin
. It is version 0.4.2
and is the one that transrate calls when it runs internally in transfuse. You don't need to download a different version as that won't do anything
--verbose
option so I can get a better understanding of what is happening please
If salmon crashes for whatever reason, like the file inputs aren't what it expects, then the message it gives is for example
Version Info: A newer version of Salmon with important new features is availaible.
Please check https://github.com/COMBINE-lab/salmon/releases, for the latest release.
Exception : [the option '--index' is required but missing]. Exiting.
So the problem is unrelated to the version as this is what v0.4.2
will always print.
Can you paste the whole error please. There should be more than just the one line you copied here...
[ERROR] 2016-02-05 05:42:30 : Version Info: A newer version of Salmon with important new features is availaible.
Please check https://github.com/COMBINE-lab/salmon/releases, for the latest release.
# salmon (alignment-based) v0.4.2
# [ program ] => salmon
# [ command ] => quant
# [ libType ] => { IU }
# [ alignments ] => { /home/ibv/jdurban/transrate_69_transcripts/Trinity_R1.fq.Trinity_R2.fq.69_transcripts.bam }
# [ targets ] => { /home/ibv/jdurban/MALPOLON/results/150807_SND405_A_L003_GZX-17/69_transcripts.fa }
# [ threads ] => { 6 }
# [ sampleOut ] => { }
# [ sampleUnaligned ] => { }
# [ output ] => { . }
# [ useVBOpt ] => { }
# [ useErrorModel ] => { }
Library format { type:paired end, relative orientation:inward, strandedness:unstranded }
Logs will be written to ./logs
numQuantThreads = 3
parseThreads = 3
Checking that provided alignment files have consistent headers . . . done
Populating targets from aln = "/home/ibv/jdurban/transrate_69_transcripts/Trinity_R1.fq.Trinity_R2.fq.69_transcripts.bam", fasta = "/home/ibv/jdurban/MALPOLON/results/150807_SND405_A_L003_GZX-17/69_transcripts.fa" . . .done
Freeing memory used by read queue . . .
Joined parsing thread . . . "/home/ibv/jdurban/transrate_69_transcripts/Trinity_R1.fq.Trinity_R2.fq.69_transcripts.bam"
Closed all files . . .
Emptied frag queue. . .
Emptied Alignemnt Group Pool. .
Emptied Alignment Group Queue. . . done
============
Exception : [Error in function boost::math::digamma<long double>(long double): Evaluation of function at pole 0]
============
/home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/bin/salmon alignment-quant was invoked improperly.
For usage information, try /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/bin/salmon quant --help-alignments
Exiting.
/home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/salmon.rb:27:in `run': Salmon failed (Transrate::SalmonError)
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:120:in `assign_and_quantify'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:63:in `run'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/transrater.rb:86:in `read_metrics'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:218:in `block (2 levels) in transrate'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:214:in `chdir'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:214:in `block in transrate'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:210:in `each'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:210:in `each_with_index'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:210:in `transrate'
from /home/ibv/jdurban/programas/transfuse-0.5.0-linux-x86_64/lib/bin/transfuse:66:in `<main>'
Exception : [Error in function boost::math::digamma<long double>(long double): Evaluation of function at pole 0]
snap
part of transrate failed and created an empty file
The alignment group queue pool has been exhausted. 0 extra fragments were allocated on the heap to saturate the pool. No new fragments will be allocated