These are chat archives for cboursnell/transfuse

5th
Feb 2016
Jordi
@jordur
Feb 05 2016 10:09
hi @cboursnell . Not sure about results. I run the following: transfuse --assemblies assembly1,assembly2 --left left_reads --right right_reads -output output_file --threads 6
firstly, the output file did not work and the output dir was the cwd
then I got the following error: [ERROR] 2016-02-05 05:42:30 : Version Info: A newer version of Salmon with important new features is availaible;
Jordi
@jordur
Feb 05 2016 10:15
And for assembly1 I got a summary.txt file from transrate but the file does not exist for assembly2.... moreover, what is the final result that I could expect? Some information would be really useful...
Chris Boursnell
@cboursnell
Feb 05 2016 10:16
The first thing transfuse does is run transrate on each of the input files and it looks like maybe that failed...
The final result you should expect is a fasta file. You can set the name of this file with --output merged.fa
Jordi
@jordur
Feb 05 2016 10:18
ok! I see. my --output parameter was a PATH file
Chris Boursnell
@cboursnell
Feb 05 2016 10:20
You will also get transrate output directories created for each input
I'll have a look at what might cause a version error warning from salmon though...
Jordi
@jordur
Feb 05 2016 10:21
yes! And I would expect a transrate result for the final merged fasta file, right?
I will install the newest version of Salmon and I will try again... I will let you know about
Chris Boursnell
@cboursnell
Feb 05 2016 10:22
You shouldn't need to isntall anything apart from the transfuse package. It contains everything you need
You did use the package from https://github.com/cboursnell/transfuse/releases yes?
Jordi
@jordur
Feb 05 2016 10:24
I got it from the link above.... yes, it is https://github.com/cboursnell/transfuse/releases/tag/v0.5.0
Chris Boursnell
@cboursnell
Feb 05 2016 10:48
This message was deleted
Chris Boursnell
@cboursnell
Feb 05 2016 10:56
I just ran transfuse through from start to finish with a new install and didn't have any problems. I'm sorry I can't reproduce this error.
The binary of salmon that is used is the one that comes in the transfuse package. It is in 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
Can you run the command again as you did before but add the --verbose option so I can get a better understanding of what is happening please
Chris Boursnell
@cboursnell
Feb 05 2016 11:05

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...

Will
@willblev
Feb 05 2016 11:11
@cboursnell Thanks for the plot- it looks promising
Jordi
@jordur
Feb 05 2016 11:12
yes, sure:
[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
I realize that in the aligments field it appears:
/home/ibv/jdurban/transrate_69_transcripts/Trinity_R1.fq.Trinity_R2.fq.69_transcripts.bam
Jordi
@jordur
Feb 05 2016 11:20
input assemblies are Trinity.Trinity.fasta and 69_transcripts.fa. And reads are Trinity_R1.fq and Trinity_R2.fq. According to this, do you think that a .bam file named Trinity_R1.fq.Trinity_R2.fq.Trinity.Trinity.bam looks fine?
anyway, I have launch transfuse again and so far a file named Trinity_R1.fq.Trinity_R2.fq.Trinity.Trinity.bam has been created.
Jordi
@jordur
Feb 05 2016 11:29
sorry, I forgot a chunk of log file:
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>'
Chris Boursnell
@cboursnell
Feb 05 2016 11:52
@rob-p Do you know what might cause Exception : [Error in function boost::math::digamma<long double>(long double): Evaluation of function at pole 0]
I've not seen this error before...
@jordur What is the size of the bam file that is created? It might have been that the snap part of transrate failed and created an empty file
Jordi
@jordur
Feb 05 2016 11:54
the created bam file is 6,4Gb. Moreover, looking at the salmon log file I have found the following:
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
btw, thank you so much for your help!!
Chris Boursnell
@cboursnell
Feb 05 2016 12:00
That's fine. salmon always prints that at the end of a log