Hi, I am executing the example mentioned on StrainPhlAN tutorial. I encounter an error while running the following command
strainphlan -s consensus_markers/*.pkl -m clade_markers/s__Eubacterium_rectale.fna -r reference_genomes/*.fna -o output -c s__Eubacterium_rectale --phylophlan_mode fast --nproc 4
The console output is as follows:
strainphlan -s consensus_markers/*.pkl -m clade_markers/s__Eubacterium_rectale.fna -r reference_genomes/*.fna -o output_samiah -c s__Eubacterium_rectale --phylophlan_mode fast --nproc 4
> Wed Jun 29 12:34:31 2022: Start StrainPhlAn 3.0 execution
> Wed Jun 29 12:34:31 2022: Creating temporary directory...
> Wed Jun 29 12:34:31 2022: Done.
> Wed Jun 29 12:34:31 2022: Getting markers from main sample files...
> Wed Jun 29 12:34:31 2022: Done.
> Wed Jun 29 12:34:31 2022: Getting markers from main reference files...Warning: [blastn] Examining 5 or more matches is recommended
> Warning: [blastn] Examining 5 or more matches is recommended
> Warning: [blastn] Examining 5 or more matches is recommended
> Warning: [blastn] Examining 5 or more matches is recommended
> Warning: [blastn] Examining 5 or more matches is recommended
> Warning: [blastn] Examining 5 or more matches is recommended
>
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Removing bad markers / samples...
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Writing samples as markers' FASTA files...
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Writing filtered clade markers as FASTA file...
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Calculating polymorphic rates...
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Executing PhyloPhlAn 3.0...
> Wed Jun 29 12:34:33 2022: Creating PhyloPhlAn 3.0 database...
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Generating PhyloPhlAn 3.0 configuration file...
> Wed Jun 29 12:34:33 2022: Done.
> Wed Jun 29 12:34:33 2022: Processing samples...
> [e] No alignments found to concatenate
>
> [e] An error was ocurred executing a external tool, exiting...
> Wed Jun 29 12:34:36 2022: Stop StrainPhlAn 3.0 execution.
The version of phyloPhlAn is 3.0.60
Please help me in solving this error.
Hi @samiahKanwar
Thanks for getting in touch. To better adress your problem, could you execute strainphlan again adding the --debug option and show us the content of the tmp* folder?
Thanks @aitor.blancomiguez . Unfortunately, --debug is not recognized by StrainPhlAn.
strainphlan -s consensus_markers/*.pkl -m clade_markers/s__Eubacterium_rectale.fna -r reference_genomes/*.fna -o output_samiah -c s__Eubacterium_rectale --phylophlan_mode fast --nproc 4 --debug
> usage: strainphlan [-h] [-d DATABASE] [-m CLADE_MARKERS]
> [-s SAMPLES [SAMPLES ...]] [-r REFERENCES [REFERENCES ...]]
> [-c CLADE] [-o OUTPUT_DIR] [-n NPROCS]
> [--secondary_samples SECONDARY_SAMPLES [SECONDARY_SAMPLES ...]]
> [--secondary_references SECONDARY_REFERENCES [SECONDARY_REFERENCES ...]]
> [--trim_sequences TRIM_SEQUENCES]
> [--marker_in_n_samples MARKER_IN_N_SAMPLES]
> [--sample_with_n_markers SAMPLE_WITH_N_MARKERS]
> [--secondary_sample_with_n_markers SECONDARY_SAMPLE_WITH_N_MARKERS]
> [--phylophlan_mode PHYLOPHLAN_MODE]
> [--phylophlan_configuration PHYLOPHLAN_CONFIGURATION]
> [--mutation_rates] [--print_clades_only]
> strainphlan: error: unrecognized arguments: --debug
Is there any other way to view the entire log?
Dear @aitor.blancomiguez
The content of tmp/* folder is as follows:
> total 56
> drwxrwxr-x 13 samiahkanwar samiahkanwar 4096 Jun 29 12:34 ./
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 msas/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 sub/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 trim_gap_perc/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 trim_not_variant/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 markers/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 markers_dna/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 map_dna/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 clean_dna/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 s__Eubacterium_rectale/
> -rw-rw-r-- 1 samiahkanwar samiahkanwar 978 Jun 29 12:34 phylophlan.cfg
> drwxrwxr-x 3 samiahkanwar samiahkanwar 4096 Jun 29 12:34 ../
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 s__Eubacterium_rectale.StrainPhlAn3/
> drwxrwxr-x 2 samiahkanwar samiahkanwar 4096 Jun 29 12:34 blastn/
Hi @samiahKanwar
If you are not able to execute the --debug parameter, it means that you do not have the latest version of MetaPhlAn/StrainPhlAn installed (version 3.0.14). Please, upgrade to the latest version and try to execute the tutorial example again. Thanks!
Thank you @aitor.blancomiguez for your reply. Yes, the older version was causing this issue. After updating to newer version of MetaPhlAn (3.0.14), the “No alignment found to concatenate” error has been resolved. Many thanks!