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TCC mtx file is not valid #40

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lambdamoses opened this issue Nov 8, 2019 · 5 comments
Closed

TCC mtx file is not valid #40

lambdamoses opened this issue Nov 8, 2019 · 5 comments

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@lambdamoses
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It seems that the mtx file for TCC matrices generated by bustools is not valid. When I tried to read the file into R with Matrix::readMM, I got this error:

Error: readMM(): column values 'j' are not in 1:nc

The column index must be wrong for some entries. For instance, for one of the files I inspected, the maximum column index is actually 738421, while the mtx file indicates 499458. Meanwhile, for that dataset, the matrix.ec file has 489048 lines.

@pmelsted
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pmelsted commented Nov 8, 2019

Can you send me a the path to where the data is, both the fastq and bus files

pmelsted added a commit that referenced this issue Nov 8, 2019
@pmelsted pmelsted closed this as completed Nov 8, 2019
@vivekbhr
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vivekbhr commented Dec 3, 2019

I am facing this issue with my data too (v0.39.4).. what was the solution?

@lambdamoses
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Pall said this problem is fixed in the development version.

@vivekbhr
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vivekbhr commented Dec 3, 2019

Thanks @lambdamoses . I'll try re-compiling from the devel branch

@vivekbhr
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vivekbhr commented Dec 3, 2019

devel branch seems to indeed fix the issue 👍

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3 participants