version 4.0 NameError: name 'no_temp' is not defined

[yl315504]

I have run pangolin for half a year. Each week I analyze Covid in DFW area. After Pangolin was updated this time, I got error complaining
"name 'no_temp' is not defined".

Below is the code I use. It was fine before Pangolin 4.0.

nohup pangolin --outdir /work/08270/yanliu74/ls6/UTSW_covid/Project_JAS_2022_03_30_COV119_11769_0/Project_JAS_2022_03_30_COV119_11769_0.trim.t0.5.ivar.fasta_pangolin_files
--outfile Project_JAS_2022_03_30_COV119_11769_0.trim.t0.5.ivar.fasta.pangolin.txt
--max-ambig 0.5 --no_temp
--tempdir /work/08270/yanliu74/ls6/UTSW_covid/Project_JAS_2022_03_30_COV119_11769_0/Project_JAS_2022_03_30_COV119_11769_0.trim.t0.5.ivar.fasta_pangolin_files
/work/08270/yanliu74/ls6/UTSW_covid/Project_JAS_2022_03_30_COV119_11769_0/Project_JAS_2022_03_30_COV119_11769_0.trim.t0.5.ivar.fasta &> output.txt &

[AngieHinrichs]

I have no idea why that would behave differently between pangolin v3 and v4, but the option should be --no-temp (with a dash) instead of --no_temp (with an underscore).

[yl315504]

It is a typo. I used "--no-temp". Please see the code below. The code works for V3, but not V4.

nohup pangolin --outdir /work/08270/yanliu74/ls6/UTSW_covid/Project_JAS_2022_03_16_COV117_11718_0/S69_pangolin_files
--outfile S69_pangolin.txt
--max-ambig 0.5 --no-temp
--tempdir /work/08270/yanliu74/ls6/UTSW_covid/Project_JAS_2022_03_16_COV117_11718_0/S69_pangolin_files
/work/08270/yanliu74/ls6/UTSW_covid/Project_JAS_2022_03_16_COV117_11718_0/S69_22C_064M0132_20220125_144_C4.bwa.trim.t0.5.ivar.fa &> output.txt &

[yl315504]

I used "--no-temp", but the error massage shows "no_temp".
NameError: name 'no_temp' is not defined

[aineniamh]

Okay, it was a bug that only shows up if the pipeline fails for another reason. I've fixed that- but I suspect there might be something else that gets flagged with this update!

[aineniamh]

Fixed now in v4.0.4!

[yl315504]

As expected, we have a new error. NameError: name 'tempdir' is not defined.

I guess this new issue was caused by other issues. Is it possible to find the real issue?

[SamaZYX]

As expected, we have a new error. NameError: name 'tempdir' is not defined.

I guess this new issue was caused by other issues. Is it possible to find the real issue?

I think it comes from a typo of variable tempdir in Line 248 and 250 in command.py . It should be args.tempdir or something like that.

And I still see the typo --no-tmp in line 56 in v4.0.4

[AngieHinrichs]

Thank you @SamaZYX for spotting those typos! Lines 248 and 250 are executed only when there was an error in an earlier stage.

@yl315504 can you send the complete output of pangolin? (You can attach the file output.txt from your command to this issue)

[yl315504]

@AngieHinrichs

I attached the output.txt and the files generated. Thanks!

output.txt

[AngieHinrichs]

OK, this line of output.txt shows the root problem:

-includeNoAltN is not a valid option

pangolin v4 is a major update including changes to the conda environment, which unfortunately are not picked up by --update. One of the conda environment changes is that ucsc-fatovcf now has a minimum version of 426. Older versions get that error about -includeNoAltN. There are other important changes in the conda environment, such as the new pangolin-data repository replacing the pangoLEARN and pango-designation repositories as the source of lineage data.

Instructions for updating your conda environment are here: https://cov-lineages.org/resources/pangolin/updating.html

[yl315504]

I re-installed the environment. It works.

Thank you guys!

[aineniamh]

I've just fixed the typos flagged by @SamaZYX there- they only get called if something else fails within the pipeline, that's how they passed the tests, note to self: must add more tests.

Sounds like the root issue was an install problem, glad it's sorted!