Dear Help
I have been running Strainphlan for the first time and followed the tutorial and manual. The first steps were successful until when I calling strainphlan to build the multiple sequence alignment and the phylogenetic tree by executing Phylophlan.
I have reinstalled Strainphlan and used the latest version. Before this version I tried with the version I installed in May 2020. The older version finalised this step, but couldn’t remove tmp file, so I decided to update Strainphlan and try again but it the newer version didn’t work though this step.
Here is my script ( I didn’t include yet any reference genome for Cutibacterium acnes):
strainphlan -s sample_markers/all/*.pkl -m strains_db_markers/s__Cutibacterium_acnes.fna -o strains_tree_Cacnes -n 4 -c s__Cutibacterium_acnes --marker_in_n_samples 40
See below the error message I got:
Tue Apr 6 16:30:11 2021: Start StrainPhlAn 3.0 execution
Tue Apr 6 16:30:11 2021: Creating temporary directory…
Tue Apr 6 16:30:11 2021: Done.
Tue Apr 6 16:30:11 2021: Getting markers from main sample files…
Tue Apr 6 16:30:14 2021: Done.
Tue Apr 6 16:30:14 2021: Getting markers from main reference files…
Tue Apr 6 16:30:15 2021: Done.
Tue Apr 6 16:30:15 2021: Removing bad markers / samples…
Tue Apr 6 16:30:15 2021: Done.
Tue Apr 6 16:30:15 2021: Writing samples as markers’ FASTA files…
Tue Apr 6 16:30:15 2021: Done.
Tue Apr 6 16:30:15 2021: Writing filtered clade markers as FASTA file…
Tue Apr 6 16:30:15 2021: Done.
Tue Apr 6 16:30:15 2021: Calculating polymorphic rates…
Tue Apr 6 16:30:16 2021: Done.
Tue Apr 6 16:30:16 2021: Executing PhyloPhlAn 3.0…
Tue Apr 6 16:30:16 2021: Creating PhyloPhlAn 3.0 database…
Tue Apr 6 16:30:16 2021: Done.
Tue Apr 6 16:30:16 2021: Generating PhyloPhlAn 3.0 configuration file…
Tue Apr 6 16:30:16 2021: Done.
Tue Apr 6 16:30:16 2021: Processing samples…
[e] expected str, bytes or os.PathLike object, not NoneType
[e] gene_markers_selection crashed
[e] An error was ocurred executing a external tool, exiting…
Tue Apr 6 16:30:50 2021: Stop StrainPhlAn 3.0 execution.
Big thanks if you can Help me!
Br, Hanna Sinkko