`callpeak`: `Error in py_module_import(module, convert = convert) : `
Closed this issue · 3 comments
I've encountered an error when running callpeak, both with my custom files and the example code included in the documentation:
Reprex
Code
eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
res <- callpeak(CHIP, CTRL, gsize = 5.2e7,
cutoff_analysis = TRUE,
outdir = tempdir(),
name = "callpeak_narrow0")Console output
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'create' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs' 'python=3.8.13' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs
added / updated specs:
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h0d85af4_4 155 KB conda-forge
ca-certificates-2022.9.24 | h033912b_0 150 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libsqlite-3.39.3 | ha978bb4_0 871 KB conda-forge
libzlib-1.2.12 | hfd90126_3 65 KB conda-forge
ncurses-6.3 | h96cf925_1 915 KB conda-forge
openssl-3.0.5 | hfd90126_2 2.5 MB conda-forge
pip-22.2.2 | pyhd8ed1ab_0 1.5 MB conda-forge
python-3.8.13 |h66c20e1_0_cpython 12.8 MB conda-forge
readline-8.1.2 | h3899abd_0 266 KB conda-forge
setuptools-65.4.0 | pyhd8ed1ab_0 731 KB conda-forge
sqlite-3.39.3 | h9ae0607_0 875 KB conda-forge
tk-8.6.12 | h5dbffcc_0 3.4 MB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
------------------------------------------------------------
Total: 24.4 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
ca-certificates conda-forge/osx-64::ca-certificates-2022.9.24-h033912b_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.39.3-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.12-hfd90126_3
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-3.0.5-hfd90126_2
pip conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.4.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.3-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'install' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs' 'python=3.8.13'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
# All requested packages already installed.
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 22.9.0
Please update conda by running
$ conda update -n base -c defaults conda
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'install' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs' '-c' 'conda-forge' 'python=3.8.13' 'numpy=1.17'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs
added / updated specs:
- numpy=1.17
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libcblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libgfortran-5.0.0 |10_4_0_h97931a8_25 146 KB conda-forge
libgfortran5-11.3.0 | h082f757_25 1.9 MB conda-forge
liblapack-3.9.0 |16_osx64_openblas 13 KB conda-forge
libopenblas-0.3.21 |openmp_h429af6e_3 9.6 MB conda-forge
llvm-openmp-14.0.4 | ha654fa7_0 329 KB conda-forge
numpy-1.17.5 | py38h6ced74f_1 5.0 MB conda-forge
python_abi-3.8 | 2_cp38 4 KB conda-forge
------------------------------------------------------------
Total: 17.0 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
numpy conda-forge/osx-64::numpy-1.17.5-py38h6ced74f_1
python_abi conda-forge/osx-64::python_abi-3.8-2_cp38
Downloading and Extracting Packages
libgfortran5-11.3.0 | 1.9 MB | ########## | 100%
libgfortran-5.0.0 | 146 KB | ########## | 100%
libopenblas-0.3.21 | 9.6 MB | ########## | 100%
libblas-3.9.0 | 13 KB | ########## | 100%
numpy-1.17.5 | 5.0 MB | ########## | 100%
llvm-openmp-14.0.4 | 329 KB | ########## | 100%
python_abi-3.8 | 4 KB | ########## | 100%
liblapack-3.9.0 | 13 KB | ########## | 100%
libcblas-3.9.0 | 13 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 22.9.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting macs3==3.0.0a6
Using cached MACS3-3.0.0a6.tar.gz (606 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting cykhash>=1.0.2
Using cached cykhash-2.0.0-cp38-cp38-macosx_10_9_x86_64.whl
Requirement already satisfied: numpy>=1.17 in /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/0.99.15/env_macs/lib/python3.8/site-packages (from macs3==3.0.0a6) (1.17.5)
Collecting Cython>=0.29
Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB)
Building wheels for collected packages: macs3
Building wheel for macs3 (pyproject.toml): started
Building wheel for macs3 (pyproject.toml): still running...
Building wheel for macs3 (pyproject.toml): finished with status 'done'
Created wheel for macs3: filename=MACS3-3.0.0a6-cp38-cp38-macosx_10_9_x86_64.whl size=1853285 sha256=aadfab20998542cff254344b0efef4878c8aa63ea308f711570f8c3fec3659ae
Stored in directory: /Users/schilder/Library/Caches/pip/wheels/95/4f/28/2ee87a153a82277a0adb1a1ab81ea9c97161e1f4eb1d9a0059
Successfully built macs3
Installing collected packages: cykhash, Cython, macs3
Successfully installed Cython-0.29.32 cykhash-2.0.0 macs3-3.0.0a6
Error
Error in py_module_import(module, convert = convert) :
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject
Session info
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MACSr_0.99.15 MACSdata_1.5.0 dplyr_1.0.10 TIPseeker_0.99.0
loaded via a namespace (and not attached):
[1] ica_1.0-3 RcppRoll_0.3.0
[3] class_7.3-20 Rsamtools_2.13.4
[5] lmtest_0.9-40 rprojroot_2.0.3
[7] crayon_1.5.1 spatstat.core_2.4-4
[9] MASS_7.3-58.1 nlme_3.1-159
[11] impute_1.71.0 basilisk_1.9.11
[13] GOSemSim_2.23.0 rlang_1.0.6
[15] XVector_0.37.1 ROCR_1.0-11
[17] readxl_1.4.1 irlba_2.3.5
[19] filelock_1.0.2 BiocParallel_1.31.12
[21] rjson_0.2.21 bit64_4.0.5
[23] glue_1.6.2 scKirby_0.1.0
[25] sctransform_0.3.5 parallel_4.2.1
[27] spatstat.sparse_2.1-1 AnnotationDbi_1.59.1
[29] BiocGenerics_0.43.4 DOSE_3.23.2
[31] spatstat.geom_2.4-0 tidyselect_1.1.2
[33] SummarizedExperiment_1.27.3 SeuratObject_4.1.2
[35] fitdistrplus_1.1-8 XML_3.99-0.10
[37] tidyr_1.2.1 zoo_1.8-11
[39] GenomicAlignments_1.33.1 xtable_1.8-4
[41] magrittr_2.0.3 evaluate_0.16
[43] ggplot2_3.3.6 cli_3.4.1
[45] zlibbioc_1.43.0 rstudioapi_0.14
[47] miniUI_0.1.1.1 sp_1.5-0
[49] rpart_4.1.16 fastmatch_1.1-3
[51] treeio_1.21.2 seqPattern_1.29.0
[53] EpiCompare_1.1.1 shiny_1.7.2
[55] xfun_0.33 ArchR_1.0.2
[57] cluster_2.1.4 genomation_1.29.0
[59] caTools_1.18.2 tidygraph_1.2.2
[61] KEGGREST_1.37.3 tibble_3.1.8
[63] interactiveDisplayBase_1.35.0 expm_0.999-6
[65] ggrepel_0.9.1 ape_5.6-2
[67] listenv_0.8.0 xlsxjars_0.6.1
[69] Biostrings_2.65.6 png_0.1-7
[71] future_1.28.0 withr_2.5.0
[73] bitops_1.0-7 ggforce_0.3.4
[75] aws.signature_0.6.0 plyr_1.8.7
[77] cellranger_1.1.0 e1071_1.7-11
[79] pillar_1.8.1 gplots_3.1.3
[81] cachem_1.0.6 GenomicFeatures_1.49.7
[83] vctrs_0.4.1 ellipsis_0.3.2
[85] generics_0.1.3 tools_4.2.1
[87] munsell_0.5.0 tweenr_2.0.2
[89] fgsea_1.23.2 aws.s3_0.3.21
[91] proxy_0.4-27 DelayedArray_0.23.2
[93] fastmap_1.1.0 compiler_4.2.1
[95] pkgload_1.3.0 abind_1.4-5
[97] httpuv_1.6.6 rtracklayer_1.57.0
[99] ExperimentHub_2.5.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[101] DescTools_0.99.46 plotly_4.10.0
[103] rgeos_0.5-9 rJava_1.0-6
[105] GenomeInfoDbData_1.2.8 gridExtra_2.3
[107] lattice_0.20-45 dir.expiry_1.5.1
[109] deldir_1.0-6 utf8_1.2.2
[111] later_1.3.0 BiocFileCache_2.5.0
[113] jsonlite_1.8.0 scales_1.2.1
[115] gld_2.6.5 tidytree_0.4.1
[117] pbapply_1.5-0 genefilter_1.79.0
[119] lazyeval_0.2.2 promises_1.2.0.1
[121] goftest_1.2-3 spatstat.utils_2.3-1
[123] reticulate_1.26 rmarkdown_2.16
[125] cowplot_1.1.1 Rtsne_0.16
[127] BSgenome_1.65.2 Biobase_2.57.1
[129] uwot_0.1.14 igraph_1.3.5
[131] survival_3.4-0 yaml_2.3.5
[133] plotrix_3.8-2 htmltools_0.5.3
[135] memoise_2.0.1 BiocIO_1.7.1
[137] Seurat_4.2.0 locfit_1.5-9.6
[139] graphlayouts_0.8.1 IRanges_2.31.2
[141] here_1.0.1 viridisLite_0.4.1
[143] digest_0.6.29 assertthat_0.2.1
[145] mime_0.12 rappdirs_0.3.3
[147] RSQLite_2.2.17 xlsx_0.6.5
[149] yulab.utils_0.0.5 future.apply_1.9.1
[151] Exact_3.2 data.table_1.14.2
[153] blob_1.2.3 S4Vectors_0.35.4
[155] splines_4.2.1 AnnotationHub_3.5.1
[157] RCurl_1.98-1.8 hms_1.1.2
[159] colorspace_2.0-3 BRGenomics_1.9.0
[161] base64enc_0.1-3 BiocManager_1.30.18
[163] GenomicRanges_1.49.1 aplot_0.1.7
[165] Signac_1.8.0 Rcpp_1.0.9
[167] RANN_2.6.1 mvtnorm_1.1-3
[169] enrichplot_1.17.2 fansi_1.0.3
[171] tzdb_0.3.0 parallelly_1.32.1
[173] ChIPseeker_1.33.2 R6_2.5.1
[175] grid_4.2.1 ggridges_0.5.4
[177] lifecycle_1.0.2 rootSolve_1.8.2.3
[179] curl_4.3.2 leiden_0.4.3
[181] DO.db_2.9 Matrix_1.5-1
[183] qvalue_2.29.0 RcppAnnoy_0.0.19
[185] RColorBrewer_1.1-3 stringr_1.4.1
[187] htmlwidgets_1.5.4 polyclip_1.10-0
[189] biomaRt_2.53.2 purrr_0.3.4
[191] shadowtext_0.1.2 gridGraphics_0.5-1
[193] mgcv_1.8-40 globals_0.16.1
[195] lmom_2.9 patchwork_1.1.2
[197] spatstat.random_2.2-0 progressr_0.11.0
[199] codetools_0.2-18 matrixStats_0.62.0
[201] GO.db_3.15.0 gtools_3.9.3
[203] prettyunits_1.1.1 dbplyr_2.2.1
[205] basilisk.utils_1.9.4 gridBase_0.4-7
[207] GenomeInfoDb_1.33.7 gtable_0.3.1
[209] DBI_1.1.3 stats4_4.2.1
[211] ggfun_0.0.7 tensor_1.5
[213] httr_1.4.4 KernSmooth_2.23-20
[215] stringi_1.7.8 progress_1.2.2
[217] reshape2_1.4.4 farver_2.1.1
[219] annotate_1.75.0 viridis_0.6.2
[221] ggtree_3.5.3 xml2_1.3.3
[223] boot_1.3-28 restfulr_0.0.15
[225] readr_2.1.2 geneplotter_1.75.0
[227] ggplotify_0.1.0 scattermore_0.8
[229] BiocVersion_3.16.0 DESeq2_1.37.6
[231] bit_4.0.4 scatterpie_0.1.8
[233] MatrixGenerics_1.9.1 spatstat.data_2.2-0
[235] ggraph_2.0.6 pkgconfig_2.0.3
[237] knitr_1.40
</details>
Hi @bschilder , macs3 version has been updated. Please try again. Thanks!
Awesome, thanks @hubentu!
Just reinstalled from GitHub and everything seems to work.
Which versions of Bioconductor were these changes pushed to?
Console output
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'create' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/1.5.2/env_macs' 'python=3.10' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/1.5.2/env_macs
added / updated specs:
- python=3.10
The following packages will be downloaded:
package | build
---------------------------|-----------------
libsqlite-3.39.4 | ha978bb4_0 870 KB conda-forge
libzlib-1.2.13 | hfd90126_4 64 KB conda-forge
pip-22.3 | pyhd8ed1ab_0 1.5 MB conda-forge
python-3.10.6 |hc14f532_0_cpython 13.4 MB conda-forge
setuptools-65.5.0 | pyhd8ed1ab_0 768 KB conda-forge
tzdata-2022e | h191b570_0 118 KB conda-forge
------------------------------------------------------------
Total: 16.6 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
ca-certificates conda-forge/osx-64::ca-certificates-2022.9.24-h033912b_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-3.0.5-hfd90126_2
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.10.6-hc14f532_0_cpython
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
tzdata conda-forge/noarch::tzdata-2022e-h191b570_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'install' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/1.5.2/env_macs' 'python=3.10'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
# All requested packages already installed.
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 22.9.0
Please update conda by running
$ conda update -n base -c defaults conda
+ '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/0/bin/conda' 'install' '--yes' '--prefix' '/Users/schilder/Library/Caches/org.R-project.R/R/basilisk/1.9.11/MACSr/1.5.2/env_macs' '-c' 'conda-forge' 'python=3.10' 'python=3.10'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
# All requested packages already installed.
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 22.9.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting macs3==3.0.0b1
Downloading MACS3-3.0.0b1.tar.gz (634 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 634.8/634.8 kB 4.5 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy>=1.23
Using cached numpy-1.23.4-cp310-cp310-macosx_10_9_x86_64.whl (18.1 MB)
Collecting hmmlearn>=0.2.8
Using cached hmmlearn-0.2.8-cp310-cp310-macosx_10_15_x86_64.whl (112 kB)
Collecting Cython>=0.29
Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB)
Collecting cykhash>=2.0
Using cached cykhash-2.0.0-cp310-cp310-macosx_10_9_x86_64.whl
Collecting scipy>=0.19
Using cached scipy-1.9.3-cp310-cp310-macosx_10_9_x86_64.whl (34.3 MB)
Collecting scikit-learn>=0.16
Using cached scikit_learn-1.1.3-cp310-cp310-macosx_10_9_x86_64.whl (8.7 MB)
Collecting joblib>=1.0.0
Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Collecting threadpoolctl>=2.0.0
Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Building wheels for collected packages: macs3
Building wheel for macs3 (pyproject.toml): started
Building wheel for macs3 (pyproject.toml): still running...
Building wheel for macs3 (pyproject.toml): finished with status 'done'
Created wheel for macs3: filename=MACS3-3.0.0b1-cp310-cp310-macosx_10_9_x86_64.whl size=2139801 sha256=87cd8a8771ed3e9b70390e624bfed83ff7ab1359432e525d3c08cf73991eb361
Stored in directory: /Users/schilder/Library/Caches/pip/wheels/ef/f9/53/e95565be8d73089241876e4cee571f925128049e2f94aaf9f0
Successfully built macs3
Installing collected packages: cykhash, threadpoolctl, numpy, joblib, Cython, scipy, scikit-learn, hmmlearn, macs3
Successfully installed Cython-0.29.32 cykhash-2.0.0 hmmlearn-0.2.8 joblib-1.2.0 macs3-3.0.0b1 numpy-1.23.4 scikit-learn-1.1.3 scipy-1.9.3 threadpoolctl-3.1.0
INFO @ Fri, 28 Oct 2022 15:52:56:
# Command line:
# ARGUMENTS LIST:
# name = callpeak_narrow0
# format = AUTO
# ChIP-seq file = ['/Users/schilder/Library/Caches/org.R-project.R/R/ExperimentHub/1453e6b6cd86c_4601']
# control file = ['/Users/schilder/Library/Caches/org.R-project.R/R/ExperimentHub/1453e36f4d18d_4606']
# effective genome size = 5.20e+07
# band width = 300
# model fold = [5.0, 50.0]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Additional cutoff on fold-enrichment is: 0.10
# Paired-End mode is off
INFO @ Fri, 28 Oct 2022 15:52:56: #1 read tag files...
INFO @ Fri, 28 Oct 2022 15:52:56: #1 read treatment tags...
INFO @ Fri, 28 Oct 2022 15:52:56: Detected format is: BED
INFO @ Fri, 28 Oct 2022 15:52:56: * Input file is gzipped.
INFO @ Fri, 28 Oct 2022 15:52:56: #1.2 read input tags...
INFO @ Fri, 28 Oct 2022 15:52:56: Detected format is: BED
INFO @ Fri, 28 Oct 2022 15:52:56: * Input file is gzipped.
INFO @ Fri, 28 Oct 2022 15:52:56: #1 tag size is determined as 101 bps
INFO @ Fri, 28 Oct 2022 15:52:56: #1 tag size = 101.0
INFO @ Fri, 28 Oct 2022 15:52:56: #1 total tags in treatment: 49622
INFO @ Fri, 28 Oct 2022 15:52:56: #1 user defined the maximum tags...
INFO @ Fri, 28 Oct 2022 15:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Fri, 28 Oct 2022 15:52:56: #1 tags after filtering in treatment: 48047
INFO @ Fri, 28 Oct 2022 15:52:56: #1 Redundant rate of treatment: 0.03
INFO @ Fri, 28 Oct 2022 15:52:56: #1 total tags in control: 50837
INFO @ Fri, 28 Oct 2022 15:52:56: #1 user defined the maximum tags...
INFO @ Fri, 28 Oct 2022 15:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Fri, 28 Oct 2022 15:52:56: #1 tags after filtering in control: 50783
INFO @ Fri, 28 Oct 2022 15:52:56: #1 Redundant rate of control: 0.00
INFO @ Fri, 28 Oct 2022 15:52:56: #1 finished!
INFO @ Fri, 28 Oct 2022 15:52:56: #2 Build Peak Model...
INFO @ Fri, 28 Oct 2022 15:52:56: #2 looking for paired plus/minus strand peaks...
INFO @ Fri, 28 Oct 2022 15:52:56: #2 Total number of paired peaks: 469
INFO @ Fri, 28 Oct 2022 15:52:56: #2 Model building with cross-correlation: Done
INFO @ Fri, 28 Oct 2022 15:52:56: #2 finished!
INFO @ Fri, 28 Oct 2022 15:52:56: #2 predicted fragment length is 228 bps
INFO @ Fri, 28 Oct 2022 15:52:56: #2 alternative fragment length(s) may be 228 bps
INFO @ Fri, 28 Oct 2022 15:52:56: #2.2 Generate R script for model : /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpOyztld/callpeak_narrow0_model.r
INFO @ Fri, 28 Oct 2022 15:52:56: #3 Call peaks...
INFO @ Fri, 28 Oct 2022 15:52:56: #3 Pre-compute pvalue-qvalue table...
INFO @ Fri, 28 Oct 2022 15:52:56: #3 Cutoff vs peaks called will be analyzed!
INFO @ Fri, 28 Oct 2022 15:52:57: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpOyztld/callpeak_narrow0_cutoff_analysis.txt'
INFO @ Fri, 28 Oct 2022 15:52:57: #3 Call peaks for each chromosome...
INFO @ Fri, 28 Oct 2022 15:52:57: #4 Write output xls file... /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpOyztld/callpeak_narrow0_peaks.xls
INFO @ Fri, 28 Oct 2022 15:52:57: #4 Write peak in narrowPeak format file... /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpOyztld/callpeak_narrow0_peaks.narrowPeak
INFO @ Fri, 28 Oct 2022 15:52:57: #4 Write summits bed file... /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpOyztld/callpeak_narrow0_summits.bed
INFO @ Fri, 28 Oct 2022 15:52:57: Done!
Hi @bschilder , the updates were pushed to bioc devel, but it just became a release version.