Run_pangolin and tree root issues - incomprehensible errors

Hi Nextstrain team,

I have a dataset which ran fine with Nextclade and able to generate a phylogenetic tree.

Now I am also trying to Nextstrain so I can get lineage as well but it turns out to be an exercise in a bit of frustration. Please check my log file.

Run-Pangolin seems to be spitting an incomprehensible error “gofasta sam” and it also cannot identify a root tree either. Wondering why so many issues with nextstrain and nextclade seems so awesome :).

Please do help.

Here is pangolin error:
Do things with sam files

gofasta sam [flags]
gofasta sam [command]

Available Commands:
indels Parse a SAM file for raw indel information
toMultiAlign Convert a SAM file to a multiple alignment in fasta format
toPairAlign convert a SAM file to pairwise alignments in fasta format
variants Call variants between ref and query from a SAM file

-h, --help help for sam
-r, --reference string Reference fasta file used to generate the sam file
-s, --samfile string samfile to read. If none is specified, will read from stdin
-t, --threads int Number of threads to use (default 1)

Use “gofasta sam [command] --help” for more information about a command.
Traceback (most recent call last):
File “/Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/snakemake/”, line 593, in snakemake
File “/Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/snakemake/”, line 1182, in include
exec(compile(code, snakefile.get_path_or_uri(), “exec”), self.globals)
File “/Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk”, line 11, in
config[“trained_model”] = os.path.join(workflow.current_basedir,’…’, config[“trained_model”])
File “/Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/”, line 76, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not LocalSourceFile
ESC[32mFound the snakefileESC[0m
ESC[32mThe query file is:ESC[0m/Users/jessie/Desktop/CompanyA/DataComb/ncov-7/results/default-build/aligned.fasta
Looking in /Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/pangoLEARN/data for data files…
Data files foundESC[0m
Trained model: /Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib
Header file: /Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib
Lineages csv: /Users/jessie/Desktop/CompanyA/DataComb/ncov-7/.snakemake/conda/e1feb4364a45ee11f40de383054aa814/lib/python3.8/site-packages/pangoLEARN/data/lineages.metadata.csv
PangolinLog.txt (END)