pangolin error

[danieljbridges]

Hi there,

I just did a fresh install of the ncov-tools environment and there appears to be an issue with pangolin. I was running a all_final_report and got the following error 2021-06-25T192934.968980.snakemake.log:

TypeError: can't pickle _thread.RLock objects [Fri Jun 25 19:28:28 2021] Error in rule make_lineage_assignments: jobid: 10 output: lineages/C30_lineage_report.csv shell: pangolin --outfile lineages/C30_lineage_report.csv qc_analysis/C30_consensus.fasta
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I ran the pangolin command in isolation in the same environment and got the same error. I then switched to another conda env with pangolin and was able to successfully generate a lineage-report from the same fasta. Any thoughts on what the issue is?

[rdeborja]

Hi Daniel,

I re-created my conda environment and ran ncov-tools with the latest versions of packages and ran it on both Illumina and ONT datasets but am unable to reproduce this issue. Is the version of pangolin, scorpio, and pangoLEARN different between the two conda environments you were using? I currently have:

pangolin 3.1.5
pangoLEARN 2021-06-15
scorpio 0.3.4

Cheers, Richard

[danieljbridges]

Hi @rdeborja,

Thanks for looking into this. I stupidly deleted my working ncov-qc environment. Have recreated it multiple times, but keep getting the same error. When I compare 'pangolin' / 'scorpio' between my 'pangolin' env (works perfectly) and my 'ncov-tools' env, they are identical to yours.

I looked closer during the environment creation and saw these errors:

SafetyError: The package for snpeff located at /home/dan/miniconda3/pkgs/snpeff-5.0-hdfd78af_1
appears to be corrupted. The path 'share/snpeff-5.0-1/snpEff.config'
has an incorrect size.
  reported size: 10773532 bytes
  actual size: 10773563 bytes

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/linux-64::tbb-2020.3-hfd86e86_0, bioconda/linux-64::usher-0.3.2-h7b4d82f_0
  path: 'lib/libtbbmalloc.so.2'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/linux-64::tbb-2020.3-hfd86e86_0, bioconda/linux-64::usher-0.3.2-h7b4d82f_0
  path: 'lib/libtbbmalloc_proxy.so.2'

I then did 'conda clean -a' and recreated the environment without any errors. Am really confused about this. Any other ideas on how to troubleshoot it?

[danieljbridges]

Ok this is clearly a install-specific issue as everything worked perfectly on another computer. After removing and reinstalling the env > 10 times, am unsure what else to do. Apologies - understand this isn't your problem, but if anyone has any suggestions or pointers, I am all ears!

[rdeborja]

Thanks for letting me know @danieljbridges. I was frantically re-installing ncov-tools and pangolin separately on various platforms but have not been able to reproduce the issue. I did encounter the same SafetyError and ClobberError but attributed it to a package caching error not associated with the issue running pangolin.

[kdmack87]

Hi Daniel - I had a similar error coming up in ncov-tools regarding snpEff. As with your case, it happened after I re-created our ncov-tools environment. Based on the error message, it was tracing back to an install of snpEff within a separate conda environment that we use (mamba-signal - https://github.com/jaleezyy/covid-19-signal). Recreating this mamba-signal environment as well cleared the snpEff safety error. Is your version of snpEff in a specific environment, or in your base environment? It might be a matter of either uninstalling or updating a conflicting version of snpEff that's located somewhere else on your system?

[danieljbridges]

Thanks all for your help and suggestions. I found out there were some pangolin packages in the base folder that appeared to be interfere with the ncov-qc environment... Everything is working well now....