SQANTI3_report.pdf generation fails when one or more structural categories are empty

[mkostich]

Hi all,

If the input isoform.gtf contains no genic_intron, genic, antisense, fusion, or intergenic isoforms (still has fsm, ism, nic, and nnic isoforms), sqanti3 runs fine till it gets to the generation of the sqanti3_report.pdf, where it fails part right after one of the 'Transcript Lengths by Subcategory' plots. Adding back the intergenic category alone avoids the problem. It would be more robust if the report generation just skips the plots with no corresponding isoforms or draws an empty plot. Error message looks like:

Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero Calls: generatePDFreport ... expand_limits_discrete_trans -> expand_limits_continuous_trans -> ifelse In addition: Warning messages: 1: The dot-dot notation (..count..) was deprecated in ggplot2 3.4.0. Please use after_stat(count) instead. 2: Removed 487 rows containing non-finite values (stat_boxplot()). 3: Removed 2776 rows containing non-finite values (stat_bin()). 4: Removed 2776 rows containing non-finite values (stat_bin()). 5: In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL Execution halted Traceback (most recent call last): File "/usr/local/bin/sqanti3_qc.py", line 2537, in <module> main() File "/usr/local/bin/sqanti3_qc.py", line 2527, in main combine_split_runs(args, split_dirs) File "/usr/local/bin/sqanti3_qc.py", line 2352, in combine_split_runs if subprocess.check_call(cmd, shell=True)!=0: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd)
Thanks for your help!

Mitch

[almart7]

Dear @mkostich , thank you for your suggestion! We will take it into account for the next release versions.