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no outputs for speciation #135

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qinghong2019 opened this issue Oct 18, 2023 · 0 comments
Open

no outputs for speciation #135

qinghong2019 opened this issue Oct 18, 2023 · 0 comments

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@qinghong2019
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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 Intra-species Diversity Analysis System
version 1.3.0; github.com/snayfach/MIDAS
Copyright (C) 2015-2016 Stephen Nayfach
Freely distributed under the GNU General Public License (GPLv3)

===========Parameters===========
Command: /homes/qinghong/miniconda3/envs/midas/bin/run_midas.py species -d ../MIDAS_ref/midas_db_v1.2 ./test -1 SRR13836152.fastq
Script: run_midas.py species
Database: ../MIDAS_ref/midas_db_v1.2
Output directory: ./test
Input reads (unpaired): SRR13836152.fastq
Remove temporary files: False
Word size for database search: 28
Minimum mapping alignment coverage: 0.75
Number of reads to use from input: use all
Number of threads for database search: 1

Aligning reads to marker-genes database
0.18 minutes
0.74 Gb maximum memory

Classifying reads
total alignments: 0
uniquely mapped reads: 0
ambiguously mapped reads: 0
0.0 minutes
0.74 Gb maximum memory

Estimating species abundance
total marker-gene coverage: 0.0
0.0 minutes
0.74 Gb maximum memory.

I know the default database is human gut microbiome, it should return some results. any help? thank you

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