Dear author, you developed a good app. When I applied it on my metagenomics samples, I came across some errors as following. Maybe you can answer my questions. Thanks a lot~
[1] "Working in: /lustre/home/liutang/41groundwater/05diversity/B12"
[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: /lustre/home/liutang/R/x86_64-pc-linux-gnu-library/3.6"
[2] "Loading libraries from: /lustre/software/R/3.6.0/gcc/7.2.0/lib64/R/library"
[1] "Libraries loaded."
[1] "Beginning MetaPop... "
[1] "Start Preprocessing: 2020-12-20 21:17:47"
[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 BCFtools"
[1] "No genes FASTA file specified. MetaPop will attempt to generate this file"
[1] "Metapop will attempt to generate a genes file using prodigal if it doesn't already exist. This message only appears if -prodigal not specified. Metapop will assume this means prodigal exists in PATH."
[1] "Attempting to make genes file..."
[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 119 files and 1 in-memory blocks...
[1] "End Preprocessing: 2020-12-21 01:40:49"
[1] "Beginning microdiversity"
[1] "Defaulting number of observations of a SNV to be called a SNP to 4"
[1] "Defaulting minimum pop. representation for a SNV to be called a SNP to 1%"
[1] "Defaulting vcf min phred call quality to 30"
[1] "No sample set as the point of reference for nucleotide calls. This is an optional setting used for time series."
[1] "Nucleotide defined as reference will be the most abundant nucleotide at each SNV locus across all samples."
[1] "Making initial SNV calls... "
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[warning] samtools mpileup option I is functional, but deprecated. Please switch to using bcftools mpileup in future.
[mpileup] 1 samples in 1 input files
[1] "done!"
Refining SNVs into SNPs... [1] "Done!"
[1] "Defaulting max sub sample size to 10."
[1] "Correcting subsamples for linked snps"
[1] "Correcting local subsamples for linked snps"
[1] "Calculating fixation index (Fst)"
Error in rbindlist(l, use.names, fill, idcol) :
Item 2 has 4 columns, inconsistent with item 1 which has 1 columns. To fill missing columns use fill=TRUE.
Calls: metapop_microdiv ... eval -> eval -> rbind -> rbind -> -> rbindlist
In addition: Warning messages:
1: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 1 has 0 rows but longest item has 1; filled with NA
2: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 2 has 0 rows but longest item has 1; filled with NA
3: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 3 has 0 rows but longest item has 1; filled with NA
Execution halted
execution time is 283min 45s
ZongzhiWu
commented
3 years ago
Dear author, you developed a good app. When I applied it on my metagenomics samples, I came across some errors as following. Maybe you can answer my questions. Thanks a lot~
[1] "Working in: /lustre/home/liutang/41groundwater/05diversity/B12" [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: /lustre/home/liutang/R/x86_64-pc-linux-gnu-library/3.6" [2] "Loading libraries from: /lustre/software/R/3.6.0/gcc/7.2.0/lib64/R/library" -> rbindlist
In addition: Warning messages:
1: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 1 has 0 rows but longest item has 1; filled with NA
2: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 2 has 0 rows but longest item has 1; filled with NA
3: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 3 has 0 rows but longest item has 1; filled with NA
Execution halted
execution time is 283min 45s
[1] "Libraries loaded." [1] "Beginning MetaPop... " [1] "Start Preprocessing: 2020-12-20 21:17:47" [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 BCFtools" [1] "No genes FASTA file specified. MetaPop will attempt to generate this file" [1] "Metapop will attempt to generate a genes file using prodigal if it doesn't already exist. This message only appears if -prodigal not specified. Metapop will assume this means prodigal exists in PATH." [1] "Attempting to make genes file..." [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 119 files and 1 in-memory blocks... [1] "End Preprocessing: 2020-12-21 01:40:49" [1] "Beginning microdiversity" [1] "Defaulting number of observations of a SNV to be called a SNP to 4" [1] "Defaulting minimum pop. representation for a SNV to be called a SNP to 1%" [1] "Defaulting vcf min phred call quality to 30" [1] "No sample set as the point of reference for nucleotide calls. This is an optional setting used for time series." [1] "Nucleotide defined as reference will be the most abundant nucleotide at each SNV locus across all samples." [1] "Making initial SNV calls... " [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 [warning] samtools mpileup option
Iis functional, but deprecated. Please switch to using bcftools mpileup in future. [mpileup] 1 samples in 1 input files [1] "done!" Refining SNVs into SNPs... [1] "Done!" [1] "Defaulting max sub sample size to 10." [1] "Correcting subsamples for linked snps" [1] "Correcting local subsamples for linked snps" [1] "Calculating fixation index (Fst)" Error in rbindlist(l, use.names, fill, idcol) : Item 2 has 4 columns, inconsistent with item 1 which has 1 columns. To fill missing columns use fill=TRUE. Calls: metapop_microdiv ... eval -> eval -> rbind -> rbind ->