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metaGmetapop / metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
MIT License
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Files issue #8

Open ebustos128 opened 3 years ago

ebustos128 commented 3 years ago

Hi, When I run the metapop pipeline I have this problem: Rscript MetaPop.R -dir ../01.bam_files/ -assem ../02.MAGs/ALL.fasta -ct ../bam.tsv -threads 12 -preprocess_only -genes ../02.MAGs/01.prodigal/ALL.ffn [1] "Working in: /home/ebustos/Escritorio/14.MetaPop/01.bam_files" [1] "Loading MetaPop Modules. This may take a minute." [1] "Modules loaded." [1] "Metapop will use the default location for R libraries during this session. This will likely fail in HPC environments." [1] "Loading Libraries..." [1] "Loading libraries from: /home/ebustos/miniconda3/lib/R/library" [1] "Libraries loaded." [1] "Only preprocessing..." [1] "Start Preprocessing: 2021-04-23 17:15:59" [1] "Metapop requires the installation location of samtools so that it may be called. Ignore this if samtools is in the path." [1] "samtools found in environment. Proceeding" [1] "Metapop requires the installation location of bcftools so that it may be called. Ignore this is bcftools is in the path." [1] "bcftools found in environment. Proceeding" [1] "Newest Samtools" [1] "Newest BCFtools" [1] "Genes are correctly formatted. Proceeding" [1] "Prodigal location specified as: " [1] "Calculating %ID over aligned region. Use flag -global to change this." [1] "Defaulting pct. ID to 95%" [1] "Defaulting minimum read length to 30 bp" [1] "Defaulting horizontal coverage (percent of bases covered at least once in a genome to be considered) to 70%" [1] "Defaulting depth truncation level to 10. Truncation level removes the top and bottom quantiles of depth of coverage over covered positions. Covers the middle 80% by default." [1] "Defaulting minimum average truncated depth (average depth of coverage over only covered positions between trunc and 1-trunc quantile, per genome) to 10" [bam_sort_core] merging from 37 files and 1 in-memory blocks... [E::fai_build_core] Format error, unexpected "1" at line 21470 samtools calmd: Failed to open reference file '../02.MAGs/ALL.fasta': No such file or directory [1] "End Preprocessing: 2021-04-23 17:27:03" Warning message: In .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec, : reading FASTA file ../02.MAGs/ALL.fasta: ignored 28513 invalid one-letter sequence codes

My Genome fasta file is a concatenate of different contigs MAGs with numerical names. The numerical name of the contigs could be a problem for metapop?

Regards, Esteban

drob2727 commented 3 years ago

When I run my command I get an issue with the MetaPop.R script. Did you upload that yourself? If so, where do I find that?

ebustos128 commented 3 years ago

You need to download the new version (1.0) of MetaPop. In this version there is the MetaPop.R file. Download from this link: https://github.com/metaGmetapop/metapop/releases/tag/v1.0