Error in simpleLoess

[sum732]

Hello !
While running Sqanti3_qc.py for one the samples I keep getting following error message:
Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, : invalid 'x' Execution halted

When this is happening, I do not get .html and .pdf along with .gff3 and .isoAnnotLite_stats.txt are not produced. All the others files are produced.

This error is happening when I am providing the -fl file. If I do not provide the -fl parameter i see all the files.

This is not an environment setup issue as in the same env another samples with -fl works, no error is shown and all the files are produced.

Next, I specifically looked at the fl clount file and compared with another samples ( that works) and all seems normal: total records are same between two files; I looked at simple stats: min max, mean, median quartiles values and expected difference are observed. I am not able to understand the error.

If any one can provide some insights that would be very helpful.

Below is the extended messages with error:

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.

Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, : invalid 'x'

Execution halted

Traceback (most recent call last):

File "Research/Programs/SQANTI3/version_5.1_Release_19_07_2022/SQANTI3-5.1/sqanti3_qc.py", line 2490, in <module>

`main()`

File "Research/Programs/SQANTI3/version_5.1_Release_19_07_2022/SQANTI3-5.1/sqanti3_qc.py", line 2473, in main
run(args)
File "Research/Programs/SQANTI3/version_5.1_Release_19_07_2022/SQANTI3-5.1/sqanti3_qc.py", line 2057, in run
if subprocess.check_call(cmd, shell=True)!=0:
File "/.conda/envs/SQANTI3.env/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/.conda/envs/SQANTI3.env/bin/Rscript /Research/Programs/SQANTI3
/version_5.1_Release_19_07_2022/SQANTI3-5.1/utilities//report_qc/SQANTI3_report.R /with_STAR_SJ_Expression/SQANTI3_QC/sqanti3_qc_2_B01_STAR_SJ_classification.txt /with_STAR_SJ_Expression/SQANTI3_QC/sqanti3_qc_2_B01_STAR_SJ_junctions.txt /with_STAR_SJ_Expression/SQANTI3_QC/sqanti3_qc_2_B01_STAR_SJ.params.txt /Research/Programs/SQANTI3/version_5.1_Release_19_07_2022/SQANTI3-5.1/utilities True both' returned non-zero exit status 1.

[sum732]

after some more testing if I remove --saturation parameter I do not see any of the errors and get all the output. So now what is causing saturation plot to fail?

[aarzalluz]

Hi @sum732 -thank you for reporting this. We will take a closer look as soon as we can. In the meantime, if running SQ3 without the --saturation parameter works for that particular sample, you will need to use that workaround in order to prevent SQ3 from failing.

[sum732]

Thanks @aarzalluz for looking into this. For now I am not producing the report with --saturation, but it would be vital to have these plots for the publication. Any help will be much appreciated.
Many thanks in advance.