telatin
commented
1 year ago Hello @sudeep71, Sorry for the late reply, I missed this. what were you using?
Closed sudeep71 closed 1 year ago
telatin
commented
1 year ago Hello @sudeep71, Sorry for the late reply, I missed this. what were you using?
Hi, I am trying to install using mamba and run this software but I am having some trouble with the phlyloseq package and R. The packages seem to be present but I get an error.
[13:14:24] Input directory "path_to/trial_reads/data/microbial/toy/example-output1/" created with Dadaist2 1.2.5 dadaist2-phyloseqMake:55 MicrobiomeAnalyst directory found: path_to/data/microbial/toy/example-output1/MicrobiomeAnalyst dadaist2-phyloseqMake:56 ERROR: R script failed with exit code 1 R version 4.0.5 (2021-03-31)
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install
conda install -y -c conda-forge mamba mamba install -y -c conda-forge -c bioconda dadaist2
dadaist2 --version dadaist2 v1.2.5
mamba list
Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge argtable2 2.13 h14c3975_1001 conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge bioconductor-biobase 2.50.0 r40hd029910_1 bioconda bioconductor-biocgenerics 0.36.0 r40hdfd78af_1 bioconda bioconductor-biocparallel 1.24.1 r40h399db7b_0 bioconda bioconductor-biomformat 1.18.0 r40hdfd78af_1 bioconda bioconductor-biostrings 2.58.0 r40hd029910_1 bioconda bioconductor-dada2 1.18.0 r40h399db7b_1 bioconda bioconductor-decipher 2.18.1 r40hd029910_0 bioconda bioconductor-delayedarray 0.16.3 r40hd029910_0 bioconda bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0 bioconda bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_2 bioconda bioconductor-genomicalignments 1.26.0 r40hd029910_1 bioconda bioconductor-genomicranges 1.42.0 r40hd029910_1 bioconda bioconductor-iranges 2.24.1 r40hd029910_0 bioconda bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 bioconda bioconductor-microbiome 1.12.0 r40hdfd78af_1 bioconda bioconductor-multtest 2.46.0 r40hd029910_1 bioconda bioconductor-phyloseq 1.34.0 r40hdfd78af_1 bioconda bioconductor-rhdf5 2.34.0 r40h399db7b_1 bioconda bioconductor-rhdf5filters 1.2.0 r40h399db7b_1 bioconda bioconductor-rhdf5lib 1.12.1 r40hd029910_0 bioconda bioconductor-rhtslib 1.22.0 r40hd029910_1 bioconda bioconductor-rsamtools 2.6.0 r40h399db7b_1 bioconda bioconductor-s4vectors 0.28.1 r40hd029910_0 bioconda bioconductor-shortread 1.48.0 r40h399db7b_1 bioconda bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1 bioconda bioconductor-xvector 0.30.0 r40hd029910_1 bioconda bioconductor-zlibbioc 1.36.0 r40hd029910_1 bioconda biom-format 2.1.10 py310h96516ba_1 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.6.15 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 ha61ee94_1011 conda-forge click 8.1.3 py310hff52083_0 conda-forge clustalo 1.2.4 h87f3376_5 bioconda commonmark 0.9.1 py_0 conda-forge curl 7.83.1 h2283fc2_0 conda-forge cutadapt 4.1 py310h1425a21_1 bioconda dadaist2 1.2.5 hdfd78af_0 bioconda dataclasses 0.8 pyhc8e2a94_3 conda-forge dnaio 0.9.1 py310h1425a21_1 bioconda expat 2.4.8 h27087fc_0 conda-forge fastp 0.23.2 hb7a2d85_2 bioconda fasttree 2.1.11 hec16e2b_1 bioconda font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.0 h8e229c2_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.10.4 hca18f0e_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge future 0.18.2 py310hff52083_5 conda-forge gcc_impl_linux-64 12.1.0 hea43390_16 conda-forge gettext 0.19.8.1 h73d1719_1008 conda-forge gfortran_impl_linux-64 12.1.0 h1db8e46_16 conda-forge glpk 5.0 h445213a_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 12.1.0 hea43390_16 conda-forge h5py 3.7.0 nompi_py310h06dffec_100 conda-forge harfbuzz 5.1.0 hf9f4e7c_0 conda-forge hdf5 1.12.1 nompi_h4df4325_104 conda-forge icu 70.1 h27087fc_0 conda-forge isa-l 2.30.0 ha770c72_4 conda-forge jpeg 9e h166bdaf_2 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h08a2579_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge lerc 3.0 h9c3ff4c_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 7.83.1 h2283fc2_0 conda-forge libdeflate 1.10 h7f98852_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.1.0 h1ec3361_16 conda-forge libgcc-ng 12.1.0 h8d9b700_16 conda-forge libgfortran-ng 12.1.0 h69a702a_16 conda-forge libgfortran5 12.1.0 hdcd56e2_16 conda-forge libglib 2.72.1 h2d90d5f_0 conda-forge libgomp 12.1.0 h8d9b700_16 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libnghttp2 1.47.0 he49606f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_0 conda-forge libpng 1.6.37 h753d276_3 conda-forge libsanitizer 12.1.0 ha89aaad_16 conda-forge libssh2 1.10.0 ha35d2d1_2 conda-forge libstdcxx-devel_linux-64 12.1.0 h1ec3361_16 conda-forge libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge libtiff 4.4.0 h0fcbabc_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.2.4 h166bdaf_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.9.14 h22db469_3 conda-forge libzip 1.9.2 hc929e4a_0 conda-forge libzlib 1.2.12 h166bdaf_2 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge make 4.3 hd18ef5c_1 conda-forge ncurses 6.3 h27087fc_1 conda-forge numpy 1.23.1 py310h53a5b5f_0 conda-forge openssl 3.0.5 h166bdaf_1 conda-forge pandas 1.4.3 py310h769672d_0 conda-forge pango 1.50.8 hc4f8a73_1 conda-forge pbzip2 1.1.13 0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pcre2 10.37 h032f7d1_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge perl-capture-tiny 0.48 pl5321ha770c72_1 conda-forge perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge perl-fastx-reader 1.5.0 pl5321hdfd78af_0 bioconda pigz 2.6 h27826a3_0 conda-forge pip 22.2.2 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pygments 2.12.0 pyhd8ed1ab_0 conda-forge python 3.10.5 ha86cf86_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-isal 1.0.1 py310h5764c6d_0 conda-forge python_abi 3.10 2_cp310 conda-forge pytz 2022.1 pyhd8ed1ab_0 conda-forge qax 0.9.6 hac521b0_1 bioconda r-ade4 1.7_19 r40h0154571_0 conda-forge r-ape 5.6_2 r40h43535f1_0 conda-forge r-assertthat 0.2.1 r40hc72bb7e_2 conda-forge r-backports 1.4.1 r40hcfec24a_0 conda-forge r-base 4.0.5 ha8c3e7c_7 conda-forge r-bh 1.78.0_0 r40hc72bb7e_0 conda-forge r-bit 4.0.4 r40hcfec24a_0 conda-forge r-bit64 4.0.5 r40hcfec24a_0 conda-forge r-bitops 1.0_7 r40h06615bd_0 conda-forge r-blob 1.2.3 r40hc72bb7e_0 conda-forge r-brio 1.1.3 r40hcfec24a_0 conda-forge r-cachem 1.0.6 r40hcfec24a_0 conda-forge r-callr 3.7.1 r40hc72bb7e_0 conda-forge r-cli 3.3.0 r40h7525677_0 conda-forge r-cluster 2.1.3 r40h8da6f51_0 conda-forge r-codetools 0.2_18 r40hc72bb7e_0 conda-forge r-colorspace 2.0_3 r40h06615bd_0 conda-forge r-crayon 1.5.1 r40hc72bb7e_0 conda-forge r-data.table 1.14.2 r40hcfec24a_0 conda-forge r-dbi 1.1.3 r40hc72bb7e_0 conda-forge r-deldir 1.0_6 r40h8da6f51_0 conda-forge r-desc 1.4.1 r40hc72bb7e_0 conda-forge r-diffobj 0.3.5 r40hcfec24a_0 conda-forge r-digest 0.6.29 r40h03ef668_0 conda-forge r-dplyr 1.0.9 r40h7525677_0 conda-forge r-ellipsis 0.3.2 r40hcfec24a_0 conda-forge r-evaluate 0.16 r40hc72bb7e_0 conda-forge r-fansi 1.0.3 r40h06615bd_0 conda-forge r-farver 2.1.1 r40h7525677_0 conda-forge r-fastmap 1.1.0 r40h03ef668_0 conda-forge r-foreach 1.5.2 r40hc72bb7e_0 conda-forge r-formatr 1.12 r40hc72bb7e_0 conda-forge r-fs 1.5.2 r40h7525677_1 conda-forge r-futile.logger 1.4.3 r40hc72bb7e_1003 conda-forge r-futile.options 1.0.1 r40hc72bb7e_1002 conda-forge r-generics 0.1.3 r40hc72bb7e_0 conda-forge r-ggplot2 3.3.6 r40hc72bb7e_0 conda-forge r-glue 1.6.2 r40h06615bd_0 conda-forge r-gtable 0.3.0 r40hc72bb7e_3 conda-forge r-hms 1.1.1 r40hc72bb7e_0 conda-forge r-hwriter 1.3.2.1 r40hc72bb7e_0 conda-forge r-igraph 1.3.4 r40hb34fc8a_0 conda-forge r-interp 1.1_3 r40h7525677_0 conda-forge r-isoband 0.2.5 r40h03ef668_0 conda-forge r-iterators 1.0.14 r40hc72bb7e_0 conda-forge r-jpeg 0.1_9 r40hcfec24a_0 conda-forge r-jsonlite 1.8.0 r40h06615bd_0 conda-forge r-labeling 0.4.2 r40hc72bb7e_1 conda-forge r-lambda.r 1.2.4 r40hc72bb7e_1 conda-forge r-lattice 0.20_45 r40hcfec24a_0 conda-forge r-latticeextra 0.6_30 r40hc72bb7e_0 conda-forge r-lifecycle 1.0.1 r40hc72bb7e_0 conda-forge r-magrittr 2.0.3 r40h06615bd_0 conda-forge r-mass 7.3_58.1 r40h06615bd_0 conda-forge r-matrix 1.3_2 r40he454529_0 conda-forge r-matrixstats 0.62.0 r40h06615bd_0 conda-forge r-memoise 2.0.1 r40hc72bb7e_0 conda-forge r-mgcv 1.8_40 r40h0154571_0 conda-forge r-munsell 0.5.0 r40hc72bb7e_1004 conda-forge r-nlme 3.1_159 r40h8da6f51_0 conda-forge r-permute 0.9_7 r40hc72bb7e_0 conda-forge r-pillar 1.8.0 r40hc72bb7e_0 conda-forge r-pixmap 0.4_12 r40hc72bb7e_0 conda-forge r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge r-pkgload 1.3.0 r40hc72bb7e_0 conda-forge r-plogr 0.2.0 r40hc72bb7e_1003 conda-forge r-plyr 1.8.7 r40h7525677_0 conda-forge r-png 0.1_7 r40hcfec24a_1004 conda-forge r-praise 1.0.0 r40hc72bb7e_1005 conda-forge r-prettyunits 1.1.1 r40hc72bb7e_1 conda-forge r-processx 3.7.0 r40h06615bd_0 conda-forge r-progress 1.2.2 r40hc72bb7e_2 conda-forge r-ps 1.7.1 r40h06615bd_0 conda-forge r-purrr 0.3.4 r40hcfec24a_1 conda-forge r-r6 2.5.1 r40hc72bb7e_0 conda-forge r-rcolorbrewer 1.1_3 r40h785f33e_0 conda-forge r-rcpp 1.0.9 r40h7525677_0 conda-forge r-rcppeigen 0.3.3.9.2 r40h43535f1_0 conda-forge r-rcppparallel 5.1.5 r40h7525677_0 conda-forge r-rcurl 1.98_1.8 r40h06615bd_0 conda-forge r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge r-reshape2 1.4.4 r40h03ef668_1 conda-forge r-rlang 1.0.4 r40h7525677_0 conda-forge r-rprojroot 2.0.3 r40hc72bb7e_0 conda-forge r-rsqlite 2.2.8 r40h03ef668_0 conda-forge r-rtsne 0.16 r40h37cf8d7_0 conda-forge r-scales 1.2.0 r40hc72bb7e_0 conda-forge r-snow 0.4_4 r40hc72bb7e_0 conda-forge r-sp 1.5_0 r40h06615bd_0 conda-forge r-stringi 1.7.8 r40h30a9eb7_0 conda-forge r-stringr 1.4.0 r40hc72bb7e_2 conda-forge r-survival 3.4_0 r40h06615bd_0 conda-forge r-testthat 3.1.4 r40h7525677_0 conda-forge r-tibble 3.1.8 r40h06615bd_0 conda-forge r-tidyr 1.2.0 r40h03ef668_0 conda-forge r-tidyselect 1.1.2 r40hc72bb7e_0 conda-forge r-utf8 1.2.2 r40hcfec24a_0 conda-forge r-vctrs 0.4.1 r40h7525677_0 conda-forge r-vegan 2.6_2 r40he5c027b_0 conda-forge r-viridislite 0.4.0 r40hc72bb7e_0 conda-forge r-waldo 0.4.0 r40hc72bb7e_0 conda-forge r-withr 2.5.0 r40hc72bb7e_0 conda-forge readline 8.1.2 h0f457ee_0 conda-forge rich 12.5.1 pyhd8ed1ab_0 conda-forge scipy 1.9.0 py310hdfbd76f_0 conda-forge sed 4.8 he412f7d_0 conda-forge seqfu 1.14.0 hbd632db_1 bioconda setuptools 63.4.3 py310hff52083_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.39.2 h4ff8645_0 conda-forge sysroot_linux-64 2.12 he073ed8_15 conda-forge tk 8.6.12 h27826a3_0 conda-forge tktable 2.10 hb7b940f_3 conda-forge typing_extensions 4.3.0 pyha770c72_0 conda-forge tzdata 2022a h191b570_0 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge xopen 1.5.0 py310hff52083_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge zip 3.0 h7f98852_1 conda-forge zlib 1.2.12 h166bdaf_2 conda-forge zstd 1.5.2 h8a70e8d_3 conda-forge
running the command
dadaist2 -i data/16S/ -o example-output1/ -m metadata.tsv -d silva_nr_v138_train_set.fa.gz --verbose -trunc-len-1 255 -trunc-len-2 224 -maxee1 2 -maxee1 2 -s1 16 -s2 24 --max-loss 0.05 --save-rds
Error
2022-08-12 13:14:22] DADA2 Finished. [2022-08-12 13:14:22] Converting dada2 taxonomy output: /tmp/dadaist2_S5cnK8/taxonomy.tsv [2022-08-12 13:14:22] 38 representative sequences found. [2022-08-12 13:14:22] DADA2 filtered 28.8127% from total 16104 to 4640 [2022-08-12 13:14:22] Multiple sequence alignment and tree generation [2022-08-12 13:14:23] Feature tree generated [2022-08-12 13:14:23] Exporting MicrobiomeAnalyst [2022-08-12 13:14:29] PhyloSeq file not generated: path_to/trial_reads/data/microbial/toy/example-output1/R/phyloseq.rds [2022-08-12 13:14:29] Diagnostics: ╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ dadaist2-phyloseqMake 1.2.5 │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ ╭─────────────────────────────────────────────────── Dadaist2: path_to/data/microbial/toy/example-output1 ───────────────────────────────────────────────────╮ │ │ │ path: path_totrial_reads/data/microbial/toy/example-output1 │ │ version: 1.2.5 │ │ valid: Yes │ │ num_otus: 38 │ │ num_samples: 3 │ │ base_files: rep-seqs.fasta, feature-table.tsv, metadata.tsv, rep-seqs.tree │ │ has_phyloseq: - │ │ has_rhea: - │ │ has_analyst: Yes path_to/trial_reads/data/microbial/toy/example-output1/MicrobiomeAnalyst │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ [13:14:24] Input directory "path_to/trial_reads/data/microbial/toy/example-output1/" created with Dadaist2 1.2.5 dadaist2-phyloseqMake:55 MicrobiomeAnalyst directory found: path_to/data/microbial/toy/example-output1/MicrobiomeAnalyst dadaist2-phyloseqMake:56 ERROR: R script failed with exit code 1 R version 4.0.5 (2021-03-31)