Tag: StrainPhlAn

Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome

Shotgun metagenomic sequencing has the potential to provide bacterial strain-level resolution which is of key importance to tackle a host of clinical questions. While bioinformatic tools that achieve strain-level resolution are available, thorough benchmarking is needed to validate their use for less investigated and low biomass microbiomes like those from…

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Encountering an error in sample2markers.py -i SRS013951.sam.bz2 -o pkl_files/ – StrainPhlAn

I am attempting to utilize Strainphlan by referring to the documentation. In Step 1, it should generate a sam.bz2 and bowtie2out.bz2 file, and indeed they are generated. However, upon proceeding to Step 2, an error regarding duplicate sequences is encountered. Interestingly, if I download the provided sam.bz2 file from the…

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Problem extracting the species marker genes from metaphlan4 database – StrainPhlAn

Hi, i met some problem extracting species marker genes from metaphlan4 database in step 2 of tutorial identifying strain transmission eventThe version information was as follows:$ strainphlan -vWed May 3 20:42:37 2023: StrainPhlAn version 4.0.3 (24 Oct 2022) when i run module load Anaconda3source activate metaphlan4module load Bowtie2 filename=$(cat ~/WORKSPACE/result/wzy/mother_infant/metaphlan4/SGB_input_transmission.txt…

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A Error occurred by running StrainPhlAn(4.0.6), this error is [Error] Phylogeny can not be inferred. Too many samples were discarded – StrainPhlAn

Yunan April 21, 2023, 11:11am 1 Dear authors, I am encountering an error when running StrainPhlAn(version=4.0.6) using the pipeline provided in the Github(StrainPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub). The error message is”[Error] Phylogeny can not be inferred. Too many samples were discarded”. I am using the data provided in…

Continue Reading A Error occurred by running StrainPhlAn(4.0.6), this error is [Error] Phylogeny can not be inferred. Too many samples were discarded – StrainPhlAn

Processing samples… error during StrainPhlAn 4 run – StrainPhlAn

Hi, @aitor.blancomiguez ,Question: I am getting the following error when running StrainPhlAn 4. I had some problems in step 5 “build the multiple sequence alignment and the phylogenetic tree”,Where could be a problem? What I should search for? Database: I’m using sample data(cmprod1.cibio.unitn.it/biobakery4/github_strainphlan4/) Command: strainphlan -s consensus_markers/*.pkl -m db_markers/t__SGB1877.fna -r…

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Too many samples discarded – StrainPhlAn

ange March 29, 2023, 8:15pm 1 Sorry, I realize this has been asked a few times for strainphlan, but I have the same problem and I could not understand which part it’s having error in. I use the most lenient settings for sample and marker threshold but it still keeps…

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Dealing with “Too many samples were discarded” – StrainPhlAn

I’m attempting to do a strainphlan analysis of Blautia wexlerae, but nothing I’m doing is working. I think the problem might be the reference genomes that I’m using, but I’m using the 2 primary genomes from NCBI. Is there another place to get correctly formatted references? Error Here’s the primary…

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PhyloPhlAn database error during StrainPhlAn 4 run – StrainPhlAn

Nadja March 15, 2023, 4:03pm 1 Hi,I am getting the following error when running StrainPhlAn 4. When running StrainPhlAn 3 on the same data there are no errors. Where could be a problem? What I should search for?‘’’Wed Mar 15 10:03:31 2023: Start StrainPhlAn 4.0.3 executionWed Mar 15 10:03:31 2023:…

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Strainphlan shallow shotgun sequencing data – StrainPhlAn

Dear, I recently tried to run strainphlan3 on shallow shotgun sequencing data of 166 skin samples (sequencing depth 12M reads). In the example, underneath, I show the phylogenetic tree of the most abundant species Cutibacterium acnes within all my samples.My first question is, can you use strainphlan3 on shallow shotgun…

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Polymorphic rate and single dominant strain – StrainPhlAn

fancyge January 28, 2023, 12:42pm #1 Hi Aitor, I wanted to ask about the .polymorphic file. Is percentage_of_polymorphic_sites the same as the term polymorphic rates? Is this calculated as number of polymorphic sites/ number of all concatenated markers? In strainphlan3, is the polymorphic_sites marked as “-“ in concatenated.aln and folder…

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StrainPhlan clade “s__Akkermansia_muciniphila” not accepted and should provide in SGB format – StrainPhlAn

raminka January 28, 2023, 1:27am #1 I want to run strainphlan4 on my metagenomics data to get the strains of the “s__Akkermansia_muciniphila”. However, following the tutorial for strainohlan4 pipeline, the clades are specified in SGB format. So I cannot pass “s__Akkermansia_muciniphila” as the option of the extract_marker step:extract_markers.py -c s__Akkermansia_muciniphilaor…

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Extract_markers.py: input database path format – StrainPhlAn

From the extract_markers.py script docs, it is not clear how the –database path should be formatted. I originally tried using 4.0.3, which is the directory name holding all of the bowtie2 db files, but I received the error: Could not locate a Bowtie index corresponding to basename “4.0”. After looking…

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