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  • Aug 30 15:10
    tropicco starred blahah/transrate
  • Aug 15 13:59
    bgruening commented #245
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  • Nov 27 2021 17:35
    Tina-L-Nguyen opened #245
  • Nov 10 2021 10:45
    timslittle closed #244
Rik
@blahah
ok
XinpengQi
@XinpengQi
Thanks! @blahah @rob-p If any testing needed from users, I would like to do it.
JakeGoodall
@JakeGoodall
Hi Transrate community. I'm hoping someone might be able to provide some advice. Similar to @Victaphanta and @sarjopp earlier in the thread I'm having issues installing all dependencies (namely Salmon_v0.4.0) using the "transrate --install-deps=all" command. As suggested further up I've tried both deleting and renaming local/bin/librt.so.1, both of which did not help. Did this issue ever get resolved? Or at the very least is there an existing/ reliable method to get salmon0.4.0 working?
Matt MacManes
@macmanes
can I hope that when TransRate is updated, @cboursnell can update TransFuse as well? Both of these are really important to my workflow, and are unreliable.. Transfuse is still using Salmon 0.4.2, giving me intractable errors
[ERROR] 2017-05-23 13:47:30 : Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
# salmon (alignment-based) v0.4.2
# [ program ] => salmon
# [ command ] => quant
# [ libType ] => { IU }
# [ alignments ] => { /mnt/lustre/macmaneslab/macmanes/orp/assemblies/transrate_1.transcripts75/1.skewer-trimmed-pair1.fastq.1.skewer-trimmed-pair2.fastq.1.transcripts75.bam }
# [ targets ] => { /mnt/lustre/macmaneslab/macmanes/orp/assemblies/1.spades_k75/1.transcripts75.fasta }
# [ threads ] => { 24 }
# [ sampleOut ] => { }
# [ sampleUnaligned ] => { }
# [ output ] => { . }
# [ useVBOpt ] => { }
# [ useErrorModel ] => { }
Library format { type:paired end, relative orientation:inward, strandedness:unstranded }
Logs will be written to ./logs
numQuantThreads = 18
parseThreads = 6
Checking that provided alignment files have consistent headers . . . done
Populating targets from aln = "/mnt/lustre/macmaneslab/macmanes/orp/assemblies/transrate_1.transcripts75/1.skewer-trimmed-pair1.fastq.1.skewer-trimmed-pair2.fastq.1.transcripts75.bam", fasta = "/mnt/lustre/macmaneslab/macmanes/orp/assemblies/1.spades_k75/1.tra
nscripts75.fasta" . . .done




processed 947385 reads in current round

/mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/salmon.rb:27:in `run': Salmon failed (Transrate::SalmonError)
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:120:in `assign_and_quantify'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:63:in `run'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/transrater.rb:86:in `read_metrics'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/lib/transfuse/transfuse.rb:218:in `block (2 levels) in transrate'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/lib/transfuse/transfuse.rb:214:in `chdir'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/lib/transfuse/transfuse.rb:214:in `block in transrate'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/lib/transfuse/transfuse.rb:210:in `each'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/lib/transfuse/transfuse.rb:210:in `each_with_index'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/libexec/lib/lib/transfuse/transfuse.rb:210:in `transrate'
    from /mnt/lustre/software/linuxbrew/colsa/Cellar/transfuse/86.64/bin/../libexec/lib/bin/transfuse:66:in `<main>'
make: *** [transfuse] Error 1

the Salmon log simply says:

[2017-05-23 13:47:28.703] [fileLog] [info] quantification processed 0 fragments so far

[2017-05-23 13:47:28.948] [fileLog] [info] quantification processed 947385 fragments so far

@rob-p @blahah

Rob Patro
@rob-p
wow --- that looks like a hard fail. Presumably a segfault, but I can't really assess from this output.
Matt MacManes
@macmanes
ya, and it’s reproducible… and 100% not worth chasing since it’s a version from 9034 years ago..
Rob Patro
@rob-p
l0l --- true. But presumably we could verify that if we run with 0.8.2 (same index and alignments) everything works?
Matt MacManes
@macmanes
Just did that.. can confirm that everything runs perfect in 0.8.2. :)
Rob Patro
@rob-p
great :) --- we'll get that fixed as soon as Richard and I can sync up. I think getting this issue resolved asap is important. The awesome selective-alignment stuff should probably wait until the subsequent release (after it's had sufficient testing within Salmon itself) ;P.
tawares07
@tawares07
Hi guys! I'm new in Linux and Transcriptome assembly. I downloaded Transrate but I really don't know how to install it. I did a "make" command but nothing happened. So, how can I install and run Transrate? (I know it's a silly question but as I told you, I'm new in Transcriptome Assembly. I hope you understand
Matt MacManes
@macmanes
There are some instructions, here, that might help: http://oyster-river-protocol.readthedocs.io/en/master/aws_setup.html
Rik
@blahah
ok so a straight salmon update to 0.8.2 should solve some things
easy to do
will try to push that out this weekend
Ilya Shlyakhter
@notestaff
Can you add a bioconda recipe for installing transrate? I've done some work on it ( https://github.com/bioconda/bioconda-recipes/tree/is-add-transrate/recipes/transrate ) but it's not working yet. The transrate gem on rubygems.org is 1.0.1 but the current version of transrate is 1.0.3 . The dependence on snap-aligner is on 1.0dev.96 , but would 1.0dev.97 work? bioconda has a build for 1.0dev.97 . Would blast+ 2.2.31 work? bioconda has a build for that, but not for 2.2.29 . In bioconda the guideline is to have a recipe for building things from source, so just fetching binaries would not work.
Austin Patton
@austinhpatton

Hi there - I've been using both Transrate and Transfuse in my assembly pipeline. In brief, I've been using three different assemblers choosing different settings within each. I then ranked each resultant assembly with Transrate and merged both within an across assemblers using Transfuse. Out of interest, I re-ranked each merged assembly using the recent version of Transrate, and what I found was that their scores did not correspond to those reported by Transfuse - they were much lower, and lower than any of the original assemblies.

I'm wondering why this might be? How does Transfuse's merging procedure differ from that of the merging implemented within Transrate? Is one preferred over the other?

Also, I haven't been able to find any documentation describing in detail what exactly Transfuse is doing. Is this available somewhere?

Thanks!

pchelych
@pchelych_twitter
Anybody home?
preeti333
@preeti333
Does this software works for paired end data only?
Rob Patro
@rob-p
@preeti333 : yes, this is currently restricted to paired-end data. The information provided by single-end data is much less useful and reliable for assembly evaluation.
Alexis Weinnig
@AMWeinnig_twitter
Hi guys, I recently read about Transrate and decided I wanted to try it for assessing a few transcriptome assemblies I have produced that don't have a reference genome. However, I looks like it is in the works for a new update and the current version isn't producing the most reliable results? Should I wait to use it until the next update is released? (I also totally understand y'all are doing this on your own time now!)
Stuart Willis
@stuartwillis
So I guess v1.0.4 is ready to rock? with updated dependencies? Any timeframe for updating the ruby gem?
Stuart Willis
@stuartwillis
ok, so deleted old local version of salmon (0.4.2) that the gem installed, copied updated version of salmon (0.8.2) there so it's in the path, and ran transrate (1.0.4) install-deps just for kicks. Got this: Checking dependencies
Installing salmon (0.4)...
[ERROR] 2017-07-20 17:13:29 : Failed to install:
  • salmon:0.4
Kate Wathen-Dunn
@katewd
@stuartwillis , I am having the same problem. Tried various salmon versions (0.4.2, 0.6.0 and 0.8.2),but I can't get TransRate to recognise them and use them, so currently I can only do the basic assembly metric analysis without the reads, etc. I would really love to get this to work, so any advice would be appreciated!
Lisa K. Johnson
@ljcohen
I had the same problem. A comment above about removing the /bin/librt.so.1 file and assistance from @bluegenes helped me out. this worked on Ubuntu 16.04: cd sudo curl -SL https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz | tar -xz cd transrate-1.0.3-linux-x86_64 ./transrate --install-deps ref rm -f bin/librt.so.1 echo 'export PATH=$PATH:"$HOME/transrate-1.0.3-linux-x86_64"', transcriptome eval tutorial here: http://dibsi-rnaseq.readthedocs.io/en/latest/evaluation.html
Kate Wathen-Dunn
@katewd
Thanks @ljcohen , you're a legend! I ran 'sudo gem uninstall transrate' , unpacked the transrate-1.0.3 tarball I already had downloaded then ran the './transrate --install-deps ref' and the 'rm librt.so.1' commands. I added the 'export PATH' line for both transrate-1.0.3 and salmon-0.8.2 to my ~/.profile and then TransRate ran perfectly. Thank you so much!
Lisa K. Johnson
@ljcohen
great, glad it worked!
Upendra Kumar Devisetty
@upendrak
Hi, I am running transrate on an Trinity assembly and eventhough the Transrate finished running and generated the outputs, I see the salmon.log file has several rows that shows this error
[2017-07-27 16:11:56.857] [jointLog] [info] Sampling alignments; outputting results to ./postSample.bam
[2017-07-27 16:11:57.184] [jointLog] [warning] [Sampler.hpp]: Failed to sample an alignment for this read; this shouldn't happen
currentMass = -nan, r = 0.293905
[2017-07-27 16:11:57.185] [jointLog] [warning] [Sampler.hpp]: Failed to sample an alignment for this read; this shouldn't happen
currentMass = -nan, r = 0.665585"
Consequently the Transrate score is quite low. Can anyone let me what this error means? Thanks..
JakeGoodall
@JakeGoodall

Hi All, I was wondering if someone could maybe weight in on an 'issue' I'm having. I've been using Translate a lot recently (great program), running lots of different assembly variants (some are TPM filter, some TransRate filtered etc, etc).

Now a consistent issue I've been having is the initial generation of the .bam file. It takes a long time (not suprising since its a massive transcriptome), but once the .bam completes (presumably) TransRate gets stuck, never moving past the .bam and/or onto the downstream analysis. Its not a massive issue, since cancelling the run, then restarting will progress the program to completion.

I wouldn’t think much off it but some of my results recently have been ‘interesting’. My best transcriptome’ initial score rated 0.8, whilst the good.assembly 1.5. Is it even possible to get TransRate scores >1? Certainly I’ve improved my ability to construct good transcriptomes as of late, but I’m more inclined to think somethings going wrong in the analysis. Should I be trusting these scores or is TransRate getting stuck affecting the outputs?

Anne Webb
@webbchen

Good morning. I've made a couple of assembly with a mixture of single- and paired end reads. The question of SE_reads came up earlier, e.g. here:

@preeti333 : yes, this is currently restricted to paired-end data. The information provided by single-end data is much less useful and reliable for assembly evaluation.

With transrate I've included the single end reads with the forward reads as I did for the assemblies. Will that cause transrate to fail? At the moment it's getting struck at the read diagnostic stage as described by Jake Goodall. Tried transrate 1.0.2 and 1.0.3 so far.
Single-ended reads are at the end of the forward-reads file so they should not interfere with the ordering of the paired-end files.
bubblegirl
@bubblegirl
@ljcohen & @katewd Thank you two! Same problem, fixed ^___^
FleurGaBru
@FleurGaBru
Hi all! I am new to transrate and have a question about the conda build. I installed transrate-tools by "conda install -c bioconda transrate-tools" but the only commando that I can execute (and can find in the conda recipes) is bam-read. I am actually looking for the commando to execute transrate to analyse my trinity assembly based on the sequences and reads. Is the conda build incomplete or do I miss something very crucial? Thanks a lot!
Matt MacManes
@macmanes
Sorry @FleurGaBru, transrate-tools is not the same as transrate.
FleurGaBru
@FleurGaBru
Thanks!
Are you planning to make a conda build for transrate?
Matt MacManes
@macmanes
that is a question for @blahah
FleurGaBru
@FleurGaBru
I actually just scrolled up a bit and saw that @notestaff is working on that. Any update on the progress?
sextuplev
@sextuplev
Dear Transrate authors and users, I am using TransRate to evaluate RNA-seq de-novo assembly and surprisingly, I got a very low mapping rate (< 1%). To check the problem, I directly used snap-aligner to map the same dataset and got a high mapping rate (>90%). In another dataset, however, TransRate gave a high mapping rate as well as snap-aligner.
I am confused now and any suggestions or solution will be appreciated.
sextuplev
@sextuplev
Hi all, I noticed that a parameter '0.95' in "bam-read in.bam out.csv 0.95", and Transrate authors use 0.7 instead. Who knows it stands for?
ddurai
@ddurai
Dear transrate authors and users. I am trying to evaluate assemblies generated by transABySS and Oases. The datasets were normalized and then assembled. I checked the transrate score for assemblies generated from various reduction levels of the normalization algorithm. The number of contigs decreased with the decrease in the number of input reads. But surprisingly, the transrate assembly score increased with the decrease in number of contigs. I am a bit confused about it. Shouldnt the transrate decrease with the decrease in the number of contigs. Or am I understanding the algorithm incorrectly. I used the original unreduced dataset for evaluation using transrate
Balázs Hajgató
@hajgato
Dear All, I would like to know how important Salmon version for transrate 1.0.3. It seems that changing from the bundled 0.6.0 to 0.8.2 gives completely different results. Which version should be used then?
Abhijeet Shah
@abshah
Hi transrate devs! I have quick question. Is there a "quick and dirty" way of getting hold of possible chimeric contigs using s(Cseg) scores ? More specifically, I mean, can I just chuck out the contigs with "low" s(Cseg) scores ?
Abhijeet Shah
@abshah
@blahah @rob-p, bump!
Rik
@blahah
@abshah sorry I haven't been getting notifications from this channel for some reason
Yes you should be able to do that. It's not a perfect filter but it fits the "quick and dirty" requirement :)
Anton Kulaga
@antonkulaga
I have misterious "terminal_columns': undefined methodwinsize' for nil:NilClass " when I run transrate blahah/transrate#216
AsterChen
@AsterChen
Hi. I recently used transrate to check my transcriptome assemblies derived from Trinity and the assembly scores were incredibly low (around 0.02). I dont know whether I did something wrongly when I run the program or my assemblies are really bad. I once changed my read files manually from .fastqsanger to .fastq since transrate seems doesnt recognize .fastqsanger. Is that a problem?