Entering edit mode
Using R 3.2.2 in Windows 8.1, I'm trying to import a qiime otu table file, using this code:
biom_otu_tax <- import_biom("D:/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom")
However, I get the error message:
Error in file(con, "r") : cannot open the connection
I have tried every combination of:
- First running setInternet2(TRUE) (this fixes it for most people)
- Setting my working directory to the file location
- Running it in R, rather than RStudio
- Opening R/RStudio as an administrator
- Restarting my computer
Nothing seems to fix it.
I feel like such an idiot, I got the file path wrong - missed a "/". However, when I corrected it I still got an error:
> biom_otu_tax <- import_biom("D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON inputThe D drive is an external hard drive plugged into my laptop. Once I corrected the file path, everything else in your post worked as expected.
OK, this indicates (possibly) that the file does not have the contents that import_biom() expects.
I'm not sure exactly beyond that. I'll ask the phyloseq maintainer to have a look at this. They may ask you to share your file so that they can try and reproduce the problem.
file.choose()provides a point-and-click way of choosing files; also, tab completion works on file paths.It worked!! Thank you!!!
This seems to have caused problems further down the line with the otu table not being read properly
When you say "this", do you mean choosing the file with file.choose() and/or tab-completion? What is the error you are getting? Is it the same one you reported earlier (invalid JSON input)? It would be helpful if you could post the complete session--all the commands you tried and R's response.
I meant file.choose(). Yes, I have been getting the same JSON error. I found another thread that suggests that this may be due to newer versions of qiime producing biom files in a different format which is not read correctly into phyloseq.
https://github.com/joey711/phyloseq/issues/443
I'll check my qiime version later (I didn't use this computer) and see if I can fix it as suggested in that thread. If not, you'll be hearing more from me soon! Thanks so much for all your help.
For reference, here is my console so far:
R version 3.2.2 (2015-08-14) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(phyloseq) > library(ggplot2) > biom_otu_tax <- import_biom("D:/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom") Error in file(con, "r") : cannot open the connection > setwd("~/Uni/2015/ECOL491/Hard drive/from_qiime/micro/results/otus_open_ref_R1") > biom_otu_tax <- import_biom("C:/Users/Moana/Documents/Uni/2015/ECOL491/Hard drive/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom") Error in file(con, "r") : cannot open the connection > file.exists("D:/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom") [1] FALSE > file.exists("C:/Users/Moana/Documents/Uni/2015/ECOL491/Hard drive/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom") [1] FALSE > file.exists("C:/Users/Moana/Documents/Uni/2015/ECOL491/Hard drive/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom") [1] TRUE > biom_otu_tax <- import_biom("D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > uzdir <- "D:/from_qiime/micro/results/otus_open_ref_R1" > otutable_biom_file <- paste(uzdir, "otu_table_mc2_w_tax_no_pynast_failures.biom", sep = "") > vzdir <- "D:/Qiime_files" > map_file <- paste(vzdir, "BaltarsurveymapR.txt", sep = "") > biom_otu_tax <- import_biom(otutable_biom_file) Error in file(con, "r") : cannot open the connection > uzdir <- "D:/from_qiime/micro/results/otus_open_ref_R1/" > otutable_biom_file <- paste(uzdir, "otu_table_mc2_w_tax_no_pynast_failures.biom", sep = "") > biom_otu_tax <- import_biom(otutable_biom_file) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > file.info("D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom") size isdir mode D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom 1729602 FALSE 666 mtime D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom 2015-10-13 17:10:28 ctime atime exe D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom 2015-10-13 17:10:28 2015-10-16 no > head(readLines("D:/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom")) Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file 'D:/from_qiime/micro/results/otus_open_ref_R1otu_table_mc2_w_tax_no_pynast_failures.biom': No such file or directory > head(readLines("D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom")) [1] "‰HDF" > example(import_biom) imprt_> # An included example of a rich dense biom file imprt_> rich_dense_biom <- system.file("extdata", "rich_dense_otu_table.biom", package="phyloseq") imprt_> import_biom(rich_dense_biom, parseFunction=parse_taxonomy_greengenes) phyloseq-class experiment-level object otu_table() OTU Table: [ 5 taxa and 6 samples ] sample_data() Sample Data: [ 6 samples by 4 sample variables ] tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ] imprt_> # An included example of a sparse dense biom file imprt_> rich_sparse_biom <- system.file("extdata", "rich_sparse_otu_table.biom", package="phyloseq") imprt_> import_biom(rich_sparse_biom, parseFunction=parse_taxonomy_greengenes) phyloseq-class experiment-level object otu_table() OTU Table: [ 5 taxa and 6 samples ] sample_data() Sample Data: [ 6 samples by 4 sample variables ] tax_table() Taxonomy Table: [ 5 taxa by 7 taxonomic ranks ] imprt_> # # # Example code for importing large file with parallel backend imprt_> # library("doParallel") imprt_> # registerDoParallel(cores=6) imprt_> # import_biom("my/file/path/file.biom", parseFunction=parse_taxonomy_greengenes, parallel=TRUE) imprt_> imprt_> imprt_> > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New Zealand.1252 LC_MONETARY=English_New Zealand.1252 [4] LC_NUMERIC=C LC_TIME=English_New Zealand.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_1.0.1 phyloseq_1.14.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.1 plyr_1.8.3 XVector_0.10.0 iterators_1.0.8 tools_3.2.2 zlibbioc_1.16.0 [7] digest_0.6.8 gtable_0.1.2 nlme_3.1-122 lattice_0.20-33 mgcv_1.8-7 Matrix_1.2-2 [13] foreach_1.4.3 igraph_1.0.1 parallel_3.2.2 proto_0.3-10 stringr_1.0.0 cluster_2.0.3 [19] Biostrings_2.38.0 S4Vectors_0.8.0 IRanges_2.4.0 stats4_3.2.2 ade4_1.7-2 multtest_2.26.0 [25] grid_3.2.2 Biobase_2.30.0 data.table_1.9.6 survival_2.38-3 RJSONIO_1.3-0 reshape2_1.4.1 [31] magrittr_1.5 scales_0.3.0 codetools_0.2-14 MASS_7.3-44 BiocGenerics_0.16.0 splines_3.2.2 [37] permute_0.8-4 colorspace_1.2-6 ape_3.3 stringi_0.5-5 munsell_0.4.2 biom_0.3.12 [43] chron_2.3-47 vegan_2.3-1 > biomot = import_biom("D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom", parseFunction = parse_taxonomy_qiime) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > biomot = import_biom(otutable_biom_file, parseFunction = parse_taxonomy_qiime) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > print(otutable_biom_file) [1] "D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom" > library(RCurl) Error in library(RCurl) : there is no package called ‘RCurl’ > library(RJSONIO) > biomot = import_biom("D:/from_qiime/micro/results/otus_open_ref_R1/otu_table_mc2_w_tax_no_pynast_failures.biom", parseFunction = parse_taxonomy_qiime) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > file.choose() [1] "C:\\Users\\Moana\\Documents\\Uni\\2015\\ECOL491\\Hard drive\\from_qiime\\micro\\results\\otus_open_ref_R1\\otu_table_mc2_w_tax_no_pynast_failures.biom" > biom_otu_tax <- file.choose() > bmsd <- import_qiime_sample_data(map_file) Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'D:/Qiime_filesBaltarsurveymapR.txt': No such file or directory > vzdir <- "D:/Qiime_files/" > map_file <- paste(vzdir, "BaltarsurveymapR.txt", sep = "") > bmsd <- import_qiime_sample_data(map_file) > class(bmsd) [1] "sample_data" attr(,"package") [1] "phyloseq" > dim(bmsd) [1] 18 27 > hlep(dim) Error: could not find function "hlep" > help(dim) > View(bmsd) > View(bmsd) > sample_data(bmsd) Sample Data: [18 samples by 27 sample variables]: SampleID BarcodeSequence LinkerPrimerSequence Depth Code Station Station_depth Zone SiteReplicate S1.1 S1.1 AACCGATGTACC CCGGACTACHVGGGTWTCTAAT Surface S1.1 1 1 Neritic S1.1 S1.2 S1.2 TCGATTGGCCGT CCGGACTACHVGGGTWTCTAAT Surface S1.2 1 1 Neritic S1.2 S2.1 S2.1 GCATTACTGGAC CCGGACTACHVGGGTWTCTAAT Surface S2.1 2 2 SubTropical S2.1 S2.2 S2.2 TTGGGCCACATA CCGGACTACHVGGGTWTCTAAT Surface S2.2 2 2 SubTropical S2.2 S3.1 S3.1 CACACAAAGTCA CCGGACTACHVGGGTWTCTAAT Surface S3.1 3 3 SubTropical S3.1 S3.2 S3.2 GCCAAGGATAGG CCGGACTACHVGGGTWTCTAAT Surface S3.2 3 3 SubTropical S3.2 S4.1 S4.1 CGCCACGTGTAT CCGGACTACHVGGGTWTCTAAT Surface S4.1 4 4 Front S4.1 S4.2 S4.2 GCAACCGATTGT CCGGACTACHVGGGTWTCTAAT Surface S4.2 4 4 Front S4.2 S5.1 S5.1 CATGTGCTTAGG CCGGACTACHVGGGTWTCTAAT Surface S5.1 5 5 Front S5.1 S5.2 S5.2 GTTCCTCCATTA CCGGACTACHVGGGTWTCTAAT Surface S5.2 5 5 Front S5.2 S6.1 S6.1 ACCTGTCCTTTC CCGGACTACHVGGGTWTCTAAT Surface S6.1 6 6 SubAntarctic S6.1 S6.2 S6.2 GTTCACGCCCAA CCGGACTACHVGGGTWTCTAAT Surface S6.2 6 6 SubAntarctic S6.2 S7.1 S7.1 CGATCGAACACT CCGGACTACHVGGGTWTCTAAT Surface S7.1 7 7 SubAntarctic S7.1 S7.2 S7.2 CATGCCAACATG CCGGACTACHVGGGTWTCTAAT Surface S7.2 7 7 SubAntarctic S7.2 S8.1 S8.1 GAGTACAGTCTA CCGGACTACHVGGGTWTCTAAT Surface S8.1 8 8 SubAntarctic S8.1 S8.2 S8.2 CCTACATGAGAC CCGGACTACHVGGGTWTCTAAT Surface S8.2 8 8 SubAntarctic S8.2 d8.1 d8.1 TCCGTGGTATAG CCGGACTACHVGGGTWTCTAAT Deep d8.1 8 8d Deep SD8.1 d8.2 d8.2 TCTACGGCACGT CCGGACTACHVGGGTWTCTAAT Deep d8.2 8 8d Deep SD8.2 distance_km_from_Taiaroa_Head Temperature_C Salinity_psu Nitrate_umol_m_3 Phosphate_umol_m_3 Silicate_umol_m_3 N_P Si_N S1.1 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S1.2 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S2.1 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S2.2 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S3.1 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S3.2 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S4.1 37.46 12.0 34.343 8.1 0.63 0.1 12.8 0.010 S4.2 37.46 12.0 34.343 8.1 0.63 0.1 12.8 0.010 S5.1 43.86 12.3 34.323 8.4 0.70 0.1 11.9 0.016 S5.2 43.86 12.3 34.323 8.4 0.70 0.1 11.9 0.016 S6.1 50.64 12.5 34.261 9.2 0.77 0.3 12.0 0.034 S6.2 50.64 12.5 34.261 9.2 0.77 0.3 12.0 0.034 S7.1 58.39 12.4 34.276 9.2 0.75 0.2 12.2 0.027 S7.2 58.39 12.4 34.276 9.2 0.75 0.2 12.2 0.027 S8.1 65.37 12.6 34.279 10.6 0.70 0.4 15.2 0.037 S8.2 65.37 12.6 34.279 10.6 0.70 0.4 15.2 0.037 d8.1 65.37 NA NA 19.1 1.30 7.5 14.6 0.394 d8.2 65.37 NA NA 19.1 1.30 7.5 14.6 0.394 Bacterial_abundance_cells__ml Bacteiral_production_ugC_l_d Community_respiration_ugC_l_d S1.1 855000 15.20 124.66 S1.2 855000 15.20 124.66 S2.1 864000 11.20 69.51 S2.2 864000 11.20 69.51 S3.1 828000 12.96 42.40 S3.2 828000 12.96 42.40 S4.1 NA 4.92 31.51 S4.2 NA 4.92 31.51 S5.1 936000 11.01 44.47 S5.2 936000 11.01 44.47 S6.1 828000 2.49 39.62 S6.2 828000 2.49 39.62 S7.1 774000 8.36 69.28 S7.2 774000 8.36 69.28 S8.1 918000 8.84 66.73 S8.2 918000 8.84 66.73 d8.1 189000 0.41 NA d8.2 189000 0.41 NA Bacterial_0.8_0.2_um_respiration_ugC_l_d morethan_0.8_um_respiration_ugC_l_d Contribution_of_bacterial_to_CR_percent S1.1 8.341782 116.32151 6.69 S1.2 8.341782 116.32151 6.69 S2.1 12.976105 56.53874 18.67 S2.2 12.976105 56.53874 18.67 S3.1 12.512673 29.89138 29.51 S3.2 12.512673 29.89138 29.51 S4.1 12.976105 18.53729 41.18 S4.2 12.976105 18.53729 41.18 S5.1 21.086171 23.38746 47.41 S5.2 21.086171 23.38746 47.41 S6.1 28.501088 11.12238 71.93 S6.2 28.501088 11.12238 71.93 S7.1 38.233166 31.04997 55.18 S7.2 38.233166 31.04997 55.18 S8.1 66.734254 0.00000 100.00 S8.2 66.734254 0.00000 100.00 d8.1 NA NA NA d8.2 NA NA NA Cell_specific_production_fmolC_cell_d Cell_sp_BR_fmolC_cell_d X_Bacterioplankton_Growth_Efficiency_percent Description S1.1 1.4810822 0.81 65 S1.1 S1.2 1.4810822 0.81 65 S1.2 S2.1 1.0803283 1.25 46 S2.1 S2.2 1.0803283 1.25 46 S2.2 S3.1 1.3045297 1.26 51 S3.1 S3.2 1.3045297 1.26 51 S3.2 S4.1 NA NA 28 S4.1 S4.2 NA NA 28 S4.2 S5.1 0.9801063 1.88 34 S5.1 S5.2 0.9801063 1.88 34 S5.2 S6.1 0.2508221 2.87 8 S6.1 S6.2 0.2508221 2.87 8 S6.2 S7.1 0.9000342 4.12 18 S7.1 S7.2 0.9000342 4.12 18 S7.2 S8.1 0.8024910 6.06 12 S8.1 S8.2 0.8024910 6.06 12 S8.2 d8.1 0.1823963 NA NA d8.1 d8.2 0.1823963 NA NA d8.2 > head(bmsd) Sample Data: [6 samples by 27 sample variables]: SampleID BarcodeSequence LinkerPrimerSequence Depth Code Station Station_depth Zone SiteReplicate S1.1 S1.1 AACCGATGTACC CCGGACTACHVGGGTWTCTAAT Surface S1.1 1 1 Neritic S1.1 S1.2 S1.2 TCGATTGGCCGT CCGGACTACHVGGGTWTCTAAT Surface S1.2 1 1 Neritic S1.2 S2.1 S2.1 GCATTACTGGAC CCGGACTACHVGGGTWTCTAAT Surface S2.1 2 2 SubTropical S2.1 S2.2 S2.2 TTGGGCCACATA CCGGACTACHVGGGTWTCTAAT Surface S2.2 2 2 SubTropical S2.2 S3.1 S3.1 CACACAAAGTCA CCGGACTACHVGGGTWTCTAAT Surface S3.1 3 3 SubTropical S3.1 S3.2 S3.2 GCCAAGGATAGG CCGGACTACHVGGGTWTCTAAT Surface S3.2 3 3 SubTropical S3.2 distance_km_from_Taiaroa_Head Temperature_C Salinity_psu Nitrate_umol_m_3 Phosphate_umol_m_3 Silicate_umol_m_3 N_P Si_N S1.1 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S1.2 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S2.1 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S2.2 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S3.1 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S3.2 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 Bacterial_abundance_cells__ml Bacteiral_production_ugC_l_d Community_respiration_ugC_l_d S1.1 855000 15.20 124.66 S1.2 855000 15.20 124.66 S2.1 864000 11.20 69.51 S2.2 864000 11.20 69.51 S3.1 828000 12.96 42.40 S3.2 828000 12.96 42.40 Bacterial_0.8_0.2_um_respiration_ugC_l_d morethan_0.8_um_respiration_ugC_l_d Contribution_of_bacterial_to_CR_percent S1.1 8.341782 116.32151 6.69 S1.2 8.341782 116.32151 6.69 S2.1 12.976105 56.53874 18.67 S2.2 12.976105 56.53874 18.67 S3.1 12.512673 29.89138 29.51 S3.2 12.512673 29.89138 29.51 Cell_specific_production_fmolC_cell_d Cell_sp_BR_fmolC_cell_d X_Bacterioplankton_Growth_Efficiency_percent Description S1.1 1.481082 0.81 65 S1.1 S1.2 1.481082 0.81 65 S1.2 S2.1 1.080328 1.25 46 S2.1 S2.2 1.080328 1.25 46 S2.2 S3.1 1.304530 1.26 51 S3.1 S3.2 1.304530 1.26 51 S3.2 > bmsd Sample Data: [18 samples by 27 sample variables]: SampleID BarcodeSequence LinkerPrimerSequence Depth Code Station Station_depth Zone SiteReplicate S1.1 S1.1 AACCGATGTACC CCGGACTACHVGGGTWTCTAAT Surface S1.1 1 1 Neritic S1.1 S1.2 S1.2 TCGATTGGCCGT CCGGACTACHVGGGTWTCTAAT Surface S1.2 1 1 Neritic S1.2 S2.1 S2.1 GCATTACTGGAC CCGGACTACHVGGGTWTCTAAT Surface S2.1 2 2 SubTropical S2.1 S2.2 S2.2 TTGGGCCACATA CCGGACTACHVGGGTWTCTAAT Surface S2.2 2 2 SubTropical S2.2 S3.1 S3.1 CACACAAAGTCA CCGGACTACHVGGGTWTCTAAT Surface S3.1 3 3 SubTropical S3.1 S3.2 S3.2 GCCAAGGATAGG CCGGACTACHVGGGTWTCTAAT Surface S3.2 3 3 SubTropical S3.2 S4.1 S4.1 CGCCACGTGTAT CCGGACTACHVGGGTWTCTAAT Surface S4.1 4 4 Front S4.1 S4.2 S4.2 GCAACCGATTGT CCGGACTACHVGGGTWTCTAAT Surface S4.2 4 4 Front S4.2 S5.1 S5.1 CATGTGCTTAGG CCGGACTACHVGGGTWTCTAAT Surface S5.1 5 5 Front S5.1 S5.2 S5.2 GTTCCTCCATTA CCGGACTACHVGGGTWTCTAAT Surface S5.2 5 5 Front S5.2 S6.1 S6.1 ACCTGTCCTTTC CCGGACTACHVGGGTWTCTAAT Surface S6.1 6 6 SubAntarctic S6.1 S6.2 S6.2 GTTCACGCCCAA CCGGACTACHVGGGTWTCTAAT Surface S6.2 6 6 SubAntarctic S6.2 S7.1 S7.1 CGATCGAACACT CCGGACTACHVGGGTWTCTAAT Surface S7.1 7 7 SubAntarctic S7.1 S7.2 S7.2 CATGCCAACATG CCGGACTACHVGGGTWTCTAAT Surface S7.2 7 7 SubAntarctic S7.2 S8.1 S8.1 GAGTACAGTCTA CCGGACTACHVGGGTWTCTAAT Surface S8.1 8 8 SubAntarctic S8.1 S8.2 S8.2 CCTACATGAGAC CCGGACTACHVGGGTWTCTAAT Surface S8.2 8 8 SubAntarctic S8.2 d8.1 d8.1 TCCGTGGTATAG CCGGACTACHVGGGTWTCTAAT Deep d8.1 8 8d Deep SD8.1 d8.2 d8.2 TCTACGGCACGT CCGGACTACHVGGGTWTCTAAT Deep d8.2 8 8d Deep SD8.2 distance_km_from_Taiaroa_Head Temperature_C Salinity_psu Nitrate_umol_m_3 Phosphate_umol_m_3 Silicate_umol_m_3 N_P Si_N S1.1 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S1.2 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S2.1 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S2.2 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S3.1 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S3.2 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S4.1 37.46 12.0 34.343 8.1 0.63 0.1 12.8 0.010 S4.2 37.46 12.0 34.343 8.1 0.63 0.1 12.8 0.010 S5.1 43.86 12.3 34.323 8.4 0.70 0.1 11.9 0.016 S5.2 43.86 12.3 34.323 8.4 0.70 0.1 11.9 0.016 S6.1 50.64 12.5 34.261 9.2 0.77 0.3 12.0 0.034 S6.2 50.64 12.5 34.261 9.2 0.77 0.3 12.0 0.034 S7.1 58.39 12.4 34.276 9.2 0.75 0.2 12.2 0.027 S7.2 58.39 12.4 34.276 9.2 0.75 0.2 12.2 0.027 S8.1 65.37 12.6 34.279 10.6 0.70 0.4 15.2 0.037 S8.2 65.37 12.6 34.279 10.6 0.70 0.4 15.2 0.037 d8.1 65.37 NA NA 19.1 1.30 7.5 14.6 0.394 d8.2 65.37 NA NA 19.1 1.30 7.5 14.6 0.394 Bacterial_abundance_cells__ml Bacteiral_production_ugC_l_d Community_respiration_ugC_l_d S1.1 855000 15.20 124.66 S1.2 855000 15.20 124.66 S2.1 864000 11.20 69.51 S2.2 864000 11.20 69.51 S3.1 828000 12.96 42.40 S3.2 828000 12.96 42.40 S4.1 NA 4.92 31.51 S4.2 NA 4.92 31.51 S5.1 936000 11.01 44.47 S5.2 936000 11.01 44.47 S6.1 828000 2.49 39.62 S6.2 828000 2.49 39.62 S7.1 774000 8.36 69.28 S7.2 774000 8.36 69.28 S8.1 918000 8.84 66.73 S8.2 918000 8.84 66.73 d8.1 189000 0.41 NA d8.2 189000 0.41 NA Bacterial_0.8_0.2_um_respiration_ugC_l_d morethan_0.8_um_respiration_ugC_l_d Contribution_of_bacterial_to_CR_percent S1.1 8.341782 116.32151 6.69 S1.2 8.341782 116.32151 6.69 S2.1 12.976105 56.53874 18.67 S2.2 12.976105 56.53874 18.67 S3.1 12.512673 29.89138 29.51 S3.2 12.512673 29.89138 29.51 S4.1 12.976105 18.53729 41.18 S4.2 12.976105 18.53729 41.18 S5.1 21.086171 23.38746 47.41 S5.2 21.086171 23.38746 47.41 S6.1 28.501088 11.12238 71.93 S6.2 28.501088 11.12238 71.93 S7.1 38.233166 31.04997 55.18 S7.2 38.233166 31.04997 55.18 S8.1 66.734254 0.00000 100.00 S8.2 66.734254 0.00000 100.00 d8.1 NA NA NA d8.2 NA NA NA Cell_specific_production_fmolC_cell_d Cell_sp_BR_fmolC_cell_d X_Bacterioplankton_Growth_Efficiency_percent Description S1.1 1.4810822 0.81 65 S1.1 S1.2 1.4810822 0.81 65 S1.2 S2.1 1.0803283 1.25 46 S2.1 S2.2 1.0803283 1.25 46 S2.2 S3.1 1.3045297 1.26 51 S3.1 S3.2 1.3045297 1.26 51 S3.2 S4.1 NA NA 28 S4.1 S4.2 NA NA 28 S4.2 S5.1 0.9801063 1.88 34 S5.1 S5.2 0.9801063 1.88 34 S5.2 S6.1 0.2508221 2.87 8 S6.1 S6.2 0.2508221 2.87 8 S6.2 S7.1 0.9000342 4.12 18 S7.1 S7.2 0.9000342 4.12 18 S7.2 S8.1 0.8024910 6.06 12 S8.1 S8.2 0.8024910 6.06 12 S8.2 d8.1 0.1823963 NA NA d8.1 d8.2 0.1823963 NA NA d8.2 > biom_otu_tax [1] "D:\\from_qiime\\micro\\results\\otus_open_ref_R1\\otu_table_mc2_w_tax_no_pynast_failures.biom" > Fede_phyloseq <- merge_phyloseq(biom_otu_tax, bmsd) > Fede_phyloseq Sample Data: [18 samples by 27 sample variables]: SampleID BarcodeSequence LinkerPrimerSequence Depth Code Station Station_depth Zone SiteReplicate S1.1 S1.1 AACCGATGTACC CCGGACTACHVGGGTWTCTAAT Surface S1.1 1 1 Neritic S1.1 S1.2 S1.2 TCGATTGGCCGT CCGGACTACHVGGGTWTCTAAT Surface S1.2 1 1 Neritic S1.2 S2.1 S2.1 GCATTACTGGAC CCGGACTACHVGGGTWTCTAAT Surface S2.1 2 2 SubTropical S2.1 S2.2 S2.2 TTGGGCCACATA CCGGACTACHVGGGTWTCTAAT Surface S2.2 2 2 SubTropical S2.2 S3.1 S3.1 CACACAAAGTCA CCGGACTACHVGGGTWTCTAAT Surface S3.1 3 3 SubTropical S3.1 S3.2 S3.2 GCCAAGGATAGG CCGGACTACHVGGGTWTCTAAT Surface S3.2 3 3 SubTropical S3.2 S4.1 S4.1 CGCCACGTGTAT CCGGACTACHVGGGTWTCTAAT Surface S4.1 4 4 Front S4.1 S4.2 S4.2 GCAACCGATTGT CCGGACTACHVGGGTWTCTAAT Surface S4.2 4 4 Front S4.2 S5.1 S5.1 CATGTGCTTAGG CCGGACTACHVGGGTWTCTAAT Surface S5.1 5 5 Front S5.1 S5.2 S5.2 GTTCCTCCATTA CCGGACTACHVGGGTWTCTAAT Surface S5.2 5 5 Front S5.2 S6.1 S6.1 ACCTGTCCTTTC CCGGACTACHVGGGTWTCTAAT Surface S6.1 6 6 SubAntarctic S6.1 S6.2 S6.2 GTTCACGCCCAA CCGGACTACHVGGGTWTCTAAT Surface S6.2 6 6 SubAntarctic S6.2 S7.1 S7.1 CGATCGAACACT CCGGACTACHVGGGTWTCTAAT Surface S7.1 7 7 SubAntarctic S7.1 S7.2 S7.2 CATGCCAACATG CCGGACTACHVGGGTWTCTAAT Surface S7.2 7 7 SubAntarctic S7.2 S8.1 S8.1 GAGTACAGTCTA CCGGACTACHVGGGTWTCTAAT Surface S8.1 8 8 SubAntarctic S8.1 S8.2 S8.2 CCTACATGAGAC CCGGACTACHVGGGTWTCTAAT Surface S8.2 8 8 SubAntarctic S8.2 d8.1 d8.1 TCCGTGGTATAG CCGGACTACHVGGGTWTCTAAT Deep d8.1 8 8d Deep SD8.1 d8.2 d8.2 TCTACGGCACGT CCGGACTACHVGGGTWTCTAAT Deep d8.2 8 8d Deep SD8.2 distance_km_from_Taiaroa_Head Temperature_C Salinity_psu Nitrate_umol_m_3 Phosphate_umol_m_3 Silicate_umol_m_3 N_P Si_N S1.1 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S1.2 15.20 14.4 34.319 0.5 0.15 1.0 3.3 2.074 S2.1 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S2.2 23.39 13.5 34.714 2.3 0.25 0.6 9.1 0.278 S3.1 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S3.2 30.36 12.5 34.541 7.1 0.59 0.2 11.9 0.028 S4.1 37.46 12.0 34.343 8.1 0.63 0.1 12.8 0.010 S4.2 37.46 12.0 34.343 8.1 0.63 0.1 12.8 0.010 S5.1 43.86 12.3 34.323 8.4 0.70 0.1 11.9 0.016 S5.2 43.86 12.3 34.323 8.4 0.70 0.1 11.9 0.016 S6.1 50.64 12.5 34.261 9.2 0.77 0.3 12.0 0.034 S6.2 50.64 12.5 34.261 9.2 0.77 0.3 12.0 0.034 S7.1 58.39 12.4 34.276 9.2 0.75 0.2 12.2 0.027 S7.2 58.39 12.4 34.276 9.2 0.75 0.2 12.2 0.027 S8.1 65.37 12.6 34.279 10.6 0.70 0.4 15.2 0.037 S8.2 65.37 12.6 34.279 10.6 0.70 0.4 15.2 0.037 d8.1 65.37 NA NA 19.1 1.30 7.5 14.6 0.394 d8.2 65.37 NA NA 19.1 1.30 7.5 14.6 0.394 Bacterial_abundance_cells__ml Bacteiral_production_ugC_l_d Community_respiration_ugC_l_d S1.1 855000 15.20 124.66 S1.2 855000 15.20 124.66 S2.1 864000 11.20 69.51 S2.2 864000 11.20 69.51 S3.1 828000 12.96 42.40 S3.2 828000 12.96 42.40 S4.1 NA 4.92 31.51 S4.2 NA 4.92 31.51 S5.1 936000 11.01 44.47 S5.2 936000 11.01 44.47 S6.1 828000 2.49 39.62 S6.2 828000 2.49 39.62 S7.1 774000 8.36 69.28 S7.2 774000 8.36 69.28 S8.1 918000 8.84 66.73 S8.2 918000 8.84 66.73 d8.1 189000 0.41 NA d8.2 189000 0.41 NA Bacterial_0.8_0.2_um_respiration_ugC_l_d morethan_0.8_um_respiration_ugC_l_d Contribution_of_bacterial_to_CR_percent S1.1 8.341782 116.32151 6.69 S1.2 8.341782 116.32151 6.69 S2.1 12.976105 56.53874 18.67 S2.2 12.976105 56.53874 18.67 S3.1 12.512673 29.89138 29.51 S3.2 12.512673 29.89138 29.51 S4.1 12.976105 18.53729 41.18 S4.2 12.976105 18.53729 41.18 S5.1 21.086171 23.38746 47.41 S5.2 21.086171 23.38746 47.41 S6.1 28.501088 11.12238 71.93 S6.2 28.501088 11.12238 71.93 S7.1 38.233166 31.04997 55.18 S7.2 38.233166 31.04997 55.18 S8.1 66.734254 0.00000 100.00 S8.2 66.734254 0.00000 100.00 d8.1 NA NA NA d8.2 NA NA NA Cell_specific_production_fmolC_cell_d Cell_sp_BR_fmolC_cell_d X_Bacterioplankton_Growth_Efficiency_percent Description S1.1 1.4810822 0.81 65 S1.1 S1.2 1.4810822 0.81 65 S1.2 S2.1 1.0803283 1.25 46 S2.1 S2.2 1.0803283 1.25 46 S2.2 S3.1 1.3045297 1.26 51 S3.1 S3.2 1.3045297 1.26 51 S3.2 S4.1 NA NA 28 S4.1 S4.2 NA NA 28 S4.2 S5.1 0.9801063 1.88 34 S5.1 S5.2 0.9801063 1.88 34 S5.2 S6.1 0.2508221 2.87 8 S6.1 S6.2 0.2508221 2.87 8 S6.2 S7.1 0.9000342 4.12 18 S7.1 S7.2 0.9000342 4.12 18 S7.2 S8.1 0.8024910 6.06 12 S8.1 S8.2 0.8024910 6.06 12 S8.2 d8.1 0.1823963 NA NA d8.1 d8.2 0.1823963 NA NA d8.2 > plot_richness(Fede_phyloseq, x = "Zone", color = "km_from_Taiaroa_Head") + geom_boxplot() Error in .nextMethod(.Object = .Object, ... = ...) : argument "taxa_are_rows" is missing, with no default In addition: Warning message: In as.matrix.data.frame(from) : Setting class(x) to NULL; result will no longer be an S4 object > View(Fede_phyloseq) > View(Fede_phyloseq) > help("plot_richness") > setwd("D:/from_qiime/micro/results/otus_open_ref_R1") > file <-import_biom(biom_otu_tax) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > map <-import_qiime_sampleData(final_otu_map) Error in read.table(file = mapfilename, header = TRUE, sep = "\t", comment.char = "") : object 'final_otu_map' not found In addition: Warning message: 'import_qiime_sampleData' is deprecated. Use 'import_qiime_sample_data' instead. See help("Deprecated") and help("phyloseq-deprecated"). > map <-import_qiime_sampleData(map_file) Warning message: 'import_qiime_sampleData' is deprecated. Use 'import_qiime_sample_data' instead. See help("Deprecated") and help("phyloseq-deprecated"). > map <-import_qiime_sample_data(map_file) > treefile <- read.tree("rep_set.tre") Error: could not find function "read.tree" > help(read.tree) > read.tree(file = "rep_set.tre") Error: could not find function "read.tree" > library(ape) > read.tree(file = "rep_set.tre") Phylogenetic tree with 5608 tips and 5606 internal nodes. Tip labels: New.CleanUp.ReferenceOTU1149, New.CleanUp.ReferenceOTU5290, New.CleanUp.ReferenceOTU19359, New.CleanUp.ReferenceOTU9154, New.CleanUp.ReferenceOTU10636, New.CleanUp.ReferenceOTU8157, ... Node labels: , 0.837, 0.983, 0.834, 0.790, 0.886, ... Unrooted; includes branch lengths. > treefile <- read.tree(file = "rep_set.tre") > run1 <-merge_phyloseq(file,map,treefile) Error in validObject(.Object) : invalid class “phyloseq” object: An otu_table is required for most analysis / graphics in the phyloseq-package > help (merge_phylose) No documentation for ‘merge_phylose’ in specified packages and libraries: you could try ‘??merge_phylose’ > help (merge_phyloseq) > file <-biom_otu_tx Error: object 'biom_otu_tx' not found > file <-biom_otu_tax > run1 <-merge_phyloseq(file,map,treefile) Error in validObject(.Object) : invalid class “phyloseq” object: An otu_table is required for most analysis / graphics in the phyloseq-package > file <-import_biom("otu_table_mc2_w_tax_no_pynast_failures.biom") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > file <-import_biom(file = "otu_table_mc2_w_tax_no_pynast_failures.biom") Error in import_biom(file = "otu_table_mc2_w_tax_no_pynast_failures.biom") : argument "BIOMfilename" is missing, with no default > file <-import_biom(BIOMfilename = "otu_table_mc2_w_tax_no_pynast_failures.biom") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > help (import_biom) > file <-import_biom(BIOMfilename="otu_table_mc2_w_tax_no_pynast_failures.biom", treefilename="rep_set.tre") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > setwd("D:/from_qiime/micro/results/otus_open_ref_R1/") > file <-import_biom(BIOMfilename="otu_table_mc2_w_tax_no_pynast_failures.biom", treefilename="rep_set.tre") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > setwd("D:\\from_qiime\\micro\\results\\otus_open_ref_R1\\") > file <-import_biom(BIOMfilename="otu_table_mc2_w_tax_no_pynast_failures.biom", treefilename="rep_set.tre") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > file <-import_biom(BIOMfilename="otu_table_mc2_w_tax_no_pynast_failures.biom", treefilename="rep_set.tre") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > biom_file = system.file("extdata", "otu_table_mc2_w_tax_no_pynast_failures.biom", package = "biom") > x = read_biom(biom_file) Error: could not find function "read_biom" > help(read_biom) > file <-import_biom(BIOMfilename="otu_table_mc2_w_tax_no_pynast_failures.biom", treefilename="rep_set.tre") Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > help("install.packages") > install.packages(biom) Error in install.packages : object 'biom' not found > install.packages(BIOM) Error in install.packages : object 'BIOM' not found Restarting R session... Loading required package: phyloseq > install.packages("biom") Error in install.packages : Updating loaded packages Restarting R session... Loading required package: phyloseq > install.packages("biom") Error in install.packages : Updating loaded packages Restarting R session... Loading required package: phyloseq > install.packages("biom") Error in install.packages : Updating loaded packages > install.packages("biom") Installing package into ‘C:/Users/Moana/Documents/R/win-library/3.2’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/biom_0.3.12.zip' Content type 'application/zip' length 158345 bytes (154 KB) downloaded 154 KB package ‘biom’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Moana\AppData\Local\Temp\RtmpYl8FoV\downloaded_packages > biom_file = system.file("extdata", "otu_table_mc2_w_tax_no_pynast_failures.biom", package = "biom") > x = read_biom(biom_file) Error: could not find function "read_biom" > library(biom) > biom_file = system.file("extdata", "otu_table_mc2_w_tax_no_pynast_failures.biom", package = "biom") > x = read_biom(biom_file) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help > biocLite("biom") BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.0), R 3.2.2 (2015-08-14). Installing package(s) ‘biom’ Warning: package ‘biom’ is in use and will not be installed Old packages: 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial' Update all/some/none? [a/s/n]: a trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/class_7.3-14.zip' Content type 'application/zip' length 99925 bytes (97 KB) downloaded 97 KB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/foreign_0.8-66.zip' Content type 'application/zip' length 288676 bytes (281 KB) downloaded 281 KB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/MASS_7.3-44.zip' Content type 'application/zip' length 1088435 bytes (1.0 MB) downloaded 1.0 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nlme_3.1-122.zip' Content type 'application/zip' length 2140460 bytes (2.0 MB) downloaded 2.0 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nnet_7.3-11.zip' Content type 'application/zip' length 121019 bytes (118 KB) downloaded 118 KB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/spatial_7.3-11.zip' Content type 'application/zip' length 151920 bytes (148 KB) downloaded 148 KB package ‘class’ successfully unpacked and MD5 sums checked package ‘foreign’ successfully unpacked and MD5 sums checked package ‘MASS’ successfully unpacked and MD5 sums checked package ‘nlme’ successfully unpacked and MD5 sums checked package ‘nnet’ successfully unpacked and MD5 sums checked package ‘spatial’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Moana\AppData\Local\Temp\RtmpYl8FoV\downloaded_packages > library(biom) > biom_file = system.file("extdata", "otu_table_mc2_w_tax_no_pynast_failures.biom", package = "biom") > x = read_biom(biom_file) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input