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Error when running the test #55
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Hi Anne-Marie, What version of Trinity are you using? Would you mind sending me your config file and a zip of the output data for Cell1 in the test output directory? Thanks! |
One more question: when you downloaded the reference mouse transcriptome, did you leave it as a zipped file rather than a plain-text fasta? If so, please unzip it and try again. This was the cause of this error previously so it might be again. |
Hi Mike,
Thanks for your response.
The mouse transcriptome is unzipped so I don’t think it’s that. I attach a zip of the cell1 directory and a copy of the config file. I have the paths to all the required software in my .profile. The Trinity version says release 2014-07-17.
Anne-Marie
… On 19 Oct 2017, at 17:44, Mike Stubbington ***@***.***> wrote:
One more question: when you downloaded the reference mouse transcriptome, did you leave it as a zipped file rather than a plain-text fasta? If so, please unzip it and try again. This was the cause of this error previously so it might be again.
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Thanks Anne-Marie. I think that Github has not been able to send me the zip file. Please could you send it directly to ms31@sanger.ac.uk ? However, I think that the problem might be that you're using a very old version of Trinity. Are you able to update to the most recent version? If not, can you use the new Docker container to run Tracer (https://github.com/teichlab/tracer#docker-image)? Thanks, Mike |
@anne-marie-lyne sent the zip directly. For completeness and future reference, I'm moving this back to Github Issues. The email message is below:
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Thanks for this Anne-Marie. Please can you check if there is a line-break in your transcriptome reference after the final ERCC sequence. From looking at your output, it seems that the first reconstructed TCRA sequence isn't being quantified by Kallisto which is possibly because it's not being properly appended to the reference transcriptome. This might be caused by a missing line break at the end of your reference file. |
PS - that error in the Trinity output seems to be caused by something new introduced in v2.5.0 but it doesn't have an effect on Trinity's use for TraCeR |
Hi Mike,
Yes, it was the lack of line break at the end of the reference fasta that was the problem. The test is now working as expected. Thank you, I certainly would never have thought of that!
Kind regards,
Anne-Marie
… On 20 Oct 2017, at 17:52, Mike Stubbington ***@***.***> wrote:
PS - that error in the Trinity output seems to be caused by something new introduced in v2.5.0 but it doesn't have an effect on Trinity's use for TraCeR
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Fantastic! Glad I could help. |
Hi,
I'm trying to run Tracer on my work cluster. It seems to run fine up until the part where it is quantifying with kallisto (or perhaps just after). Below is the last part of the error message. Any thoughts on what the problem could be?
Thanks,
Anne-Marie
.
.
.
##Quantifying with Kallisto##
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 109,377
[index] number of k-mers: 95,790,004
[index] number of equivalence classes: 392,009
[quant] running in paired-end mode
[quant] will process pair 1: /bioinfo/users/alyne/tracer-master/test_data/cell1_1.fastq
/bioinfo/users/alyne/tracer-master/test_data/cell1_2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,135 reads, 1,042 reads pseudoaligned
[quant] estimated average fragment length: 106.333
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 52 rounds
Traceback (most recent call last):
File "tracer", line 21, in
launch()
File "/bioinfo/users/alyne/tracer-master/tracerlib/launcher.py", line 43, in launch
Task().run()
File "/bioinfo/users/alyne/tracer-master/tracerlib/tasks.py", line 1198, in run
loci=['A', 'B'], max_junc_len=50).run()
File "/bioinfo/users/alyne/tracer-master/tracerlib/tasks.py", line 369, in run
self.quantify(cell)
File "/bioinfo/users/alyne/tracer-master/tracerlib/tasks.py", line 635, in quantify
tpm = counts[receptor][locus][rec.contig_name]
KeyError: 'c0_g1_i2'
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