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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…
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…
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…
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…
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…
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…
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…
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:…
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…
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…
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…
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…