MIDAS
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snayfach
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
Hi, I run "run_midas.py species" with the default database with gut metagenomics and fastq from SRR13836152 (human gut microbiome). no results at all. everytime it has the message: MIDAS: Metagenomic...
Hello, I have installed MIDAS using conda command in an empty virtual environment. I also installed samtools under the same conda environment. The installation is a success. But when I...
Hi, When I want to build a 30 species pangenome database for snp calling, I meet some errors. fna and other files were downloaded from PATRIC database. I found that...
Hello, running > run_midas.py genes Goes well but in the end, I get: E::idx_fin_and_load Could not retrieve index file for 'midas_output//genes/temp/pangenomes.bam' And then when I run: > run_midas.py snps Goes...
I'm trying to run the `MIDAS` pipeline using a Python 2 environment configured for use with `MIDAS`. My main environment is a `Python 3.6` environment and it looks like the...
Hello, I'm very new to MIDAS and also Linux. Can you please help me with this error? When I run `test_midas.py -vf`, RunSNPs always fail. What's the problem here? FAIL:...
I was running midas as a module, module load midas /1.3.2 I encountered this error Error: could not execute samtools binary: samtools (exited with error code 127) To solve this...
I mange applications on a research cluster and our researchers have been reporting issues with execution speed of your software on out cluster. I have just run through the first...
Per the snp_diversity.py script, documentation states: Only quantify diversity at synonymous sites (Note: use the ratio of 5/6 for pN/pS) What does this mean? Is pN/pS calculated by running: snp_diversity.py...
Hi, when I ran test_midas.py, I received an error message for the RunSNPs test. Do you potentially know what is causing this? ====================================================================== FAIL: test_class (__main__._07_RunSNPs) ---------------------------------------------------------------------- Traceback (most recent...
