Hi ! First I want to thank you for this wonderful, useful and detailed software! This is remarkable for the research in replication timing.
And I really want to try out your packages in our linux server. The version of R-base(3.6.3) and the packages are a bit old so it takes me a while to fully install all the requirements. But when I tried to run the Kronos binning function, it comes with an error and I don't know how to solve this.
My command line is :"
Kronos binning -R /data2/database/mm10/Genome/Genome.fa -i /data2/database/mm10/Genome/Genome -B /data2/database/mm10/Genome/Genome/BlackList.bed --bin_size 20000 --paired_ends -o /data4/fang/cell_cycle/HiRES/embryo_ecto_neurotube/pipeline_test/kronos/ -c 4 "
The reference genome and bowtie are cool. and the error comes with :"
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
[1] TRUE
[1] TRUE
Error in UseMethod("mutate") :
no applicable method for 'mutate' applied to an object of class "NULL"
Calls: %>% -> select -> group_by -> mutate
Execution halted "
And the output of simulated .bam file are small.
Could you please help me with this? Thank you very much
This is the session INFO in my R env for kronos：
R version 3.6.3 (2020-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /data4/fang/opt/anaconda3/envs/R363/lib/libopenblasp-r0.3.28.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rbowtie2_1.8.0 Rsamtools_2.2.3 Biostrings_2.54.0
[4] XVector_0.26.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[7] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[10] DNAcopy_1.60.0 gplots_3.2.0 MASS_7.3-51
[13] Cairo_1.6-2 scales_1.3.0 LaplacesDemon_16.1.6
[16] RColorBrewer_1.1-3 Rtsne_0.17 matrixStats_1.4.1
[19] optparse_1.7.5 forcats_1.0.0 stringr_1.5.1
[22] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[25] tidyr_1.1.0 tibble_3.2.1 ggplot2_3.3.0
[28] tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.2 modelr_0.1.8
[4] gtools_3.9.5 assertthat_0.2.1 GenomeInfoDbData_1.2.2
[7] cellranger_1.1.0 pillar_1.9.0 backports_1.2.1
[10] glue_1.8.0 rvest_1.0.4 colorspace_2.1-1
[13] pkgconfig_2.0.3 broom_0.7.0 haven_2.3.0
[16] zlibbioc_1.32.0 getopt_1.20.4 BiocParallel_1.20.1
[19] tzdb_0.1.2 generics_0.1.3 withr_3.0.2
[22] cli_3.6.3 magrittr_2.0.1 crayon_1.4.1
[25] readxl_1.3.1 fs_1.5.0 fansi_0.4.2
[28] xml2_1.3.2 tools_3.6.3 hms_1.1.3
[31] lifecycle_1.0.4 munsell_0.5.1 reprex_2.1.1
[34] compiler_3.6.3 caTools_1.18.3 rlang_1.1.2
[37] grid_3.6.3 RCurl_1.98-1.16 rstudioapi_0.13
[40] bitops_1.0-9 gtable_0.3.0 DBI_1.2.3
[43] R6_2.5.0 lubridate_1.7.9 utf8_1.2.1
[46] KernSmooth_2.23-24 stringi_1.6.2 Rcpp_1.0.6
[49] vctrs_0.6.5 dbplyr_2.0.0 tidyselect_1.2.1
Hi ! First I want to thank you for this wonderful, useful and detailed software! This is remarkable for the research in replication timing.
And I really want to try out your packages in our linux server. The version of R-base(3.6.3) and the packages are a bit old so it takes me a while to fully install all the requirements. But when I tried to run the Kronos binning function, it comes with an error and I don't know how to solve this.
My command line is :"
Kronos binning -R /data2/database/mm10/Genome/Genome.fa -i /data2/database/mm10/Genome/Genome -B /data2/database/mm10/Genome/Genome/BlackList.bed --bin_size 20000 --paired_ends -o /data4/fang/cell_cycle/HiRES/embryo_ecto_neurotube/pipeline_test/kronos/ -c 4 "
The reference genome and bowtie are cool. and the error comes with :"
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
[1] TRUE
[1] TRUE
Error in UseMethod("mutate") :
no applicable method for 'mutate' applied to an object of class "NULL"
Calls: %>% -> select -> group_by -> mutate
Execution halted "
And the output of simulated .bam file are small.
Could you please help me with this? Thank you very much
This is the session INFO in my R env for kronos：
R version 3.6.3 (2020-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /data4/fang/opt/anaconda3/envs/R363/lib/libopenblasp-r0.3.28.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rbowtie2_1.8.0 Rsamtools_2.2.3 Biostrings_2.54.0
[4] XVector_0.26.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[7] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[10] DNAcopy_1.60.0 gplots_3.2.0 MASS_7.3-51
[13] Cairo_1.6-2 scales_1.3.0 LaplacesDemon_16.1.6
[16] RColorBrewer_1.1-3 Rtsne_0.17 matrixStats_1.4.1
[19] optparse_1.7.5 forcats_1.0.0 stringr_1.5.1
[22] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[25] tidyr_1.1.0 tibble_3.2.1 ggplot2_3.3.0
[28] tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.2 modelr_0.1.8
[4] gtools_3.9.5 assertthat_0.2.1 GenomeInfoDbData_1.2.2
[7] cellranger_1.1.0 pillar_1.9.0 backports_1.2.1
[10] glue_1.8.0 rvest_1.0.4 colorspace_2.1-1
[13] pkgconfig_2.0.3 broom_0.7.0 haven_2.3.0
[16] zlibbioc_1.32.0 getopt_1.20.4 BiocParallel_1.20.1
[19] tzdb_0.1.2 generics_0.1.3 withr_3.0.2
[22] cli_3.6.3 magrittr_2.0.1 crayon_1.4.1
[25] readxl_1.3.1 fs_1.5.0 fansi_0.4.2
[28] xml2_1.3.2 tools_3.6.3 hms_1.1.3
[31] lifecycle_1.0.4 munsell_0.5.1 reprex_2.1.1
[34] compiler_3.6.3 caTools_1.18.3 rlang_1.1.2
[37] grid_3.6.3 RCurl_1.98-1.16 rstudioapi_0.13
[40] bitops_1.0-9 gtable_0.3.0 DBI_1.2.3
[43] R6_2.5.0 lubridate_1.7.9 utf8_1.2.1
[46] KernSmooth_2.23-24 stringi_1.6.2 Rcpp_1.0.6
[49] vctrs_0.6.5 dbplyr_2.0.0 tidyselect_1.2.1