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ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes
GNU General Public License v3.0
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[BUG] Error running qc #309

Closed nkliutx closed 4 months ago

nkliutx commented 4 months ago

Is there an existing issue for this?

Have you loaded the SQANTI3.env conda environment?

Problem description

I'm running sqanti3_qc.py, and it cannot generate full report files. I ran the command below to reproduce the error. It seems like no ism found caused this error.

Code sample

/usr/bin/Rscript /home/bio/data2/ovseqs/longread/sqanti3/SQANTI3/utilities//report_qc/SQANTI3_report.R /home/bio/data2/ovseqs/longread/sqanti3/SQANTI3/result/bambu/bam_classification.txt /home/bio/data2/ovseqs/longread/sqanti3/SQANTI3/result/bambu/bam_junctions.txt /home/bio/data2/ovseqs/longread/sqanti3/SQANTI3/result/bambu/bam.params.txt /home/bio/data2/ovseqs/longread/sqanti3/SQANTI3/utilities True both

Error

Warning message: The size argument of element_line() is deprecated as of ggplot2 3.4.0. ℹ Please use the linewidth argument instead. Warning message: Using size aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use linewidth instead. Warning message: A numeric legend.position argument in theme() was deprecated in ggplot2 3.5.0. ℹ Please use the legend.position.inside argument of theme() instead. summarise() has grouped output by 'lenCat'. You can override using the .groups argument. summarise() has grouped output by 'associated_transcript'. You can override using the .groups argument. summarise() has grouped output by 'associated_transcript'. You can override using the .groups argument. [[1]]

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[1] "SQANTI3 report successfully generated!" In addition: There were 11 warnings (use warnings() to see them)

processing file: SQANTI3_report.Rmd |................ | 66% [unnamed-chunk-31] Quitting from lines 884-912 [unnamed-chunk-31] (SQANTI3_report.Rmd) Error in ans[ypos] <- rep(yes, length.out = len)[ypos]: ! replacement has length zero Backtrace:

  1. ggplotly(cage_hist_ISM) %>% ...
  2. plotly:::ggplotly.ggplot(cage_hist_ISM)
  3. plotly::gg2list(...)
  4. plotly (local) ggplotly_build(p)
  5. layout$setup_panel_params() ...
    1. ggplot2:::expand_limits_scale(scale, expansion, limits, coord_limits = coord_limits)
    2. ggplot2:::expand_limits_discrete(...)
    3. ggplot2:::expand_limits_discrete_trans(...)
    4. ggplot2:::expand_limits_continuous_trans(...)
    5. base::ifelse(is.na(coord_limits), limits, coord_limits)

Anything else?

This is the classfication.txt 35 antisense 37202 full-splice_match 11 fusion 13 genic 11 genic_intron 438 intergenic 319 novel_in_catalog 193 novel_not_in_catalog 1 structural_category

alexpan00 commented 4 months ago

Hi,

yes, some of the plots assume that you have a particular structural category, in this case, ISM, and when the SC is not present it can crash. We are working to avoid this kind of crash, but is not a priority. You can comment those lines in the SQANTI3_report.R and it should work. If you have used polyA motifs it may also crash there.

Sorry for the inconvenience, Alejandro