Files issue

[ebustos128]

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]

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]

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