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RajLabMSSM / echolocatoR

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
https://rajlabmssm.github.io/echolocatoR
MIT License
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finemap_loci fails outside the MAGMA.CellTyping container #110

Closed AMCalejandro closed 1 year ago

AMCalejandro commented 1 year ago

1. Bug description

I am running the basic pipeline, and it fails outside the MAGMA.Celltyping container.

2. Reproducible example

Code

topSNPs <- echodata::topSNPs_Nalls2019
fullSS_path <- echodata::example_fullSS(dataset = "Nalls2019")

res <- echolocatoR::finemap_loci(
  fullSS_path = fullSS_path,
  topSNPs = topSNPs,
  loci = c("BST1","MEX3C"),
  finemap_methods = c("ABF","FINEMAP","SUSIE"),
  dataset_name = "Nalls23andMe_2019",
  fullSS_genome_build = "hg19",
  bp_distance = 10000,
  munged = TRUE,
  conda_env = "echoverse"
  )

Console output

┌────────────────────────────────────────┐
│                                        │
│   )))> 🦇 BST1 [locus 1 / 2] 🦇 <(((   │
│                                        │
└────────────────────────────────────────┘

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Step 1 ▶▶▶ Query 🔎 ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────+ Query Method: tabix
Constructing GRanges query using min/max ranges within a single chromosome.
query_dat is already a GRanges object. Returning directly.
========= echotabix::convert =========
Converting full summary stats file to tabix format for fast querying.
Inferred format: 'table'
Explicit format: 'table'
Inferring comment_char from tabular header: 'SNP'
Determining chrom type from file header.
Assuming fullSS_path summary stats have already been processed with MungeSumstats.
Chromosome format: 1
Detecting column delimiter.
Identified column separator: \t
Sorting rows by coordinates via bash.
Searching for header row with grep.
( grep ^'SNP' .../nalls2019.fullSS_subset.tsv; grep
    -v ^'SNP' .../nalls2019.fullSS_subset.tsv | sort
    -k2,2n
    -k3,3n ) > .../file320c8c784fed17_sorted.tsv
Constructing outputs
Selecting valid alternative method: conda
bgzipping file with conda.
echoconda:: conda already installed.
Retrieving conda env name from yaml:
a character vector argument expectedLocus BST1 complete in: 0.01 min
┌─────────────────────────────────────────┐
│                                         │
│   )))> 🦇 MEX3C [locus 2 / 2] 🦇 <(((   │
│                                         │
└─────────────────────────────────────────┘

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Step 1 ▶▶▶ Query 🔎 ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────+ Query Method: tabix
Constructing GRanges query using min/max ranges within a single chromosome.
query_dat is already a GRanges object. Returning directly.
========= echotabix::convert =========
Converting full summary stats file to tabix format for fast querying.
Inferred format: 'table'
Explicit format: 'table'
Inferring comment_char from tabular header: 'SNP'
Determining chrom type from file header.
Chromosome format: 1
Detecting column delimiter.
Identified column separator: \t
Sorting rows by coordinates via bash.
Searching for header row with grep.
( grep ^'SNP' .../nalls2019.fullSS_subset.tsv; grep
    -v ^'SNP' .../nalls2019.fullSS_subset.tsv | sort
    -k2,2n
    -k3,3n ) > .../file320c8c2cc7fa90_sorted.tsv
Constructing outputs
Selecting valid alternative method: conda
bgzipping file with conda.
echoconda:: conda already installed.
Retrieving conda env name from yaml:
a character vector argument expectedLocus MEX3C complete in: 0 min

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Step 6 ▶▶▶ Postprocess data 🎁 ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────Returning results as nested list.
All loci done in: 0.01 min
Warning messages:
1: In rhtslib_warning(method = method, rhtslib_pkgs = rhtslib_pkgs,  :
  The selected method (rsamtools) depends on Rhtslib, and the version you have installed (1.26.0) contains known bugs. Please install Rhtslib >=1.99.2 via Bioconductor >=3.16:
    BiocManager::install(version='devel')
2: In rhtslib_warning(method = method, rhtslib_pkgs = rhtslib_pkgs,  :
  The selected method (rsamtools) depends on Rhtslib, and the version you have installed (1.26.0) contains known bugs. Please install Rhtslib >=1.99.2 via Bioconductor >=3.16:
    BiocManager::install(version='devel')

> res
$BST1
NULL

$MEX3C
NULL

$merged_dat
Null data.table (0 rows and 0 cols)

Data

topSNPs Locus Gene CHR POS SNP P Effect 1: ASXL3 ASXL3 18 31304318 rs1941685 1.69e-08 0.0531 2: BAG3 BAG3 10 121415685 rs72840788 1.57e-11 0.0763 3: BIN3 BIN3 8 22525980 rs2280104 1.16e-08 0.0556 4: BRIP1 BRIP1 17 59917366 rs61169879 9.28e-10 0.0820 5: BST1 BST1 4 15737348 rs4698412 2.06e-28 0.1035 6: C5orf24 C5orf24 5 134199105 rs11950533 7.16e-09 -0.0916 7: CAB39L CAB39L 13 49927732 rs9568188 1.15e-08 0.0617 8: CAMK2D CAMK2D 4 114369065 rs13117519 9.82e-13 0.0875 9: CASC16 CASC16 16 52636242 rs3104783 1.29e-12 0.0668 10: CD19 CD19 16 28944396 rs2904880 7.87e-10 -0.0650 11: CHD9 CHD9 16 52969426 rs10221156 1.08e-10 -0.1156 12: CHRNB1 CHRNB1 17 7355621 rs12600861 1.01e-08 -0.0565 13: CLCN3 CLCN3 4 170583157 rs62333164 2.00e-10 -0.0638 14: CNTN1 CNTN1 12 40936639 rs141128804 6.38e-14 0.3468 15: CRHR1 CRHR1 17 43744203 rs62053943 3.58e-68 -0.2700 16: CRLS1 CRLS1 20 6006041 rs77351827 8.87e-09 0.0802 17: CTSB CTSB 8 11712443 rs1293298 3.99e-16 0.0930 18: DDRGK1 DDRGK1 20 3164686 rs2295545 8.45e-11 0.0622 19: DLG2 DLG2 11 83487277 rs12283611 2.61e-10 -0.0645 20: DNAH17 DNAH17 17 76425480 rs666463 3.20e-09 0.0760 21: DYRK1A DYRK1A 21 38852361 rs2248244 2.74e-11 0.0714 22: ELOVL7 ELOVL7 5 60137959 rs1867598 2.52e-23 -0.1554 23: FAM171A2 FAM171A2 17 42434630 rs850738 1.29e-11 -0.0710 24: FAM47E FAM47E 4 77147969 rs4101061 4.97e-19 -0.0912 25: FAM47E-STBD1 FAM47E-STBD1 4 77198054 rs6854006 5.82e-21 -0.0912 26: FAM49B FAM49B 8 130901909 rs2086641 1.81e-08 -0.0605 27: FBRSL1 FBRSL1 12 133063768 rs11610045 1.77e-10 0.0601 28: FCGR2A FCGR2A 1 161469054 rs6658353 6.10e-12 0.0650 29: FGD4 FGD4 12 32810759 rs181609621 7.69e-11 -0.4232 30: FGF20 FGF20 8 16697593 rs620513 2.72e-15 -0.0856 31: FYN FYN 6 112243291 rs997368 1.84e-09 0.0714 32: GAK GAK 4 925376 rs873786 1.79e-21 -0.1731 33: GALC GALC 14 88464264 rs979812 6.19e-11 0.0610 34: GBAP1 GBAP1 1 155205634 rs76763715 1.59e-22 -0.7467 35: GBF1 GBF1 10 104015279 rs10748818 1.05e-09 -0.0790 36: GCH1 GCH1 14 55348869 rs11158026 1.66e-16 -0.0842 37: GPNMB GPNMB 7 23300049 rs199351 5.25e-26 0.1016 38: GS1-124K5.11 GS1-124K5.11 7 66009851 rs76949143 1.43e-08 -0.1432 39: GXYLT1 GXYLT1 12 42295779 rs138017112 7.29e-12 0.4130 40: HIP1R HIP1R 12 123326598 rs10847864 1.47e-37 0.1478 41: HLA-DRB5 HLA-DRB5 6 32578772 rs112485576 6.96e-28 -0.1676 42: IGSF9B IGSF9B 11 133787001 rs3802920 6.26e-20 0.1073 43: INPP5F INPP5F 10 121536327 rs117896735 2.36e-28 0.4354 44: IP6K2 IP6K2 3 48748989 rs12497850 1.36e-10 0.0636 45: ITGA8 ITGA8 10 15557406 rs896435 3.41e-13 0.0735 46: ITPKB ITPKB 1 226916078 rs4653767 1.38e-15 0.0833 47: KANSL1 KANSL1 17 44189067 rs7225002 1.84e-40 0.1351 48: KCNIP3 KCNIP3 2 96000943 rs2042477 1.38e-08 -0.0657 49: KCNS3 KCNS3 2 18147848 rs76116224 1.27e-08 0.1104 50: KPNA1 KPNA1 3 122196892 rs55961674 9.98e-12 0.0861 51: KRTCAP2 KRTCAP2 1 155135036 rs35749011 1.72e-70 0.6068 52: LCORL LCORL 4 17968811 rs34025766 2.87e-10 -0.0839 53: LINC00693 LINC00693 3 28705690 rs6808178 8.09e-12 0.0658 54: LOC100131289 LOC100131289 6 27738801 rs4140646 5.62e-12 0.0833 55: LRRK2 LRRK2 12 40614434 rs76904798 1.52e-28 0.1439 56: MAP3K14 MAP3K14 17 43417273 rs17686238 8.25e-27 -0.1896 57: MAP4K4 MAP4K4 2 102396963 rs11683001 8.04e-13 0.0705 58: MAPT-AS1 MAPT-AS1 17 43933307 rs7221167 1.36e-37 0.1443 59: MBNL2 MBNL2 13 97865021 rs4771268 1.45e-09 0.0675 60: MCCC1 MCCC1 3 182760073 rs10513789 1.22e-34 0.1485 61: MED12L MED12L 3 151108965 rs11707416 1.13e-10 -0.0627 62: MEX3C MEX3C 18 48683589 rs8087969 1.41e-08 -0.0578 63: MIPOL1 MIPOL1 14 37989270 rs12147950 3.54e-08 -0.0529 64: NOD2 NOD2 16 50736656 rs6500328 1.82e-09 0.0586 65: NSF NSF 17 44800946 rs199453 8.62e-67 -0.2045 66: NUCKS1 NUCKS1 1 205723572 rs823118 1.11e-29 0.1066 67: PAM PAM 5 102365794 rs26431 1.57e-09 0.0621 68: PMVK PMVK 1 154898185 rs114138760 4.19e-09 0.2812 69: RAB29 RAB29 1 205737739 rs11557080 2.50e-22 0.1315 70: RETREG3 RETREG3 17 40741013 rs12951632 1.40e-09 0.0642 71: RIMS1 RIMS1 6 72487762 rs12528068 1.63e-10 0.0657 72: RIT2 RIT2 18 40673380 rs12456492 3.80e-23 -0.0983 73: RNF141 RNF141 11 10558777 rs7938782 2.12e-09 0.0870 74: RPS12 RPS12 6 133210361 rs75859381 1.04e-10 -0.2207 75: RPS6KL1 RPS6KL1 14 75373034 rs3742785 1.92e-09 0.0707 76: SATB1 SATB1 3 18361759 rs73038319 5.94e-13 -0.1693 77: SCAF11 SCAF11 12 46419086 rs7134559 3.96e-08 -0.0539 78: SCARB2 SCARB2 4 77110365 rs6825004 1.17e-09 0.0622 79: SEMA4A SEMA4A 1 156154860 rs35643925 8.11e-22 0.3890 80: SETD1A SETD1A 16 30977799 rs11150601 5.12e-20 0.0907 81: SH3GL2 SH3GL2 9 17579690 rs13294100 8.72e-18 -0.0859 82: SIPA1L2 SIPA1L2 1 232664611 rs10797576 6.84e-17 0.1114 83: SLC44A4 SLC44A4 6 31846234 rs9267659 3.65e-11 0.0790 84: SNCA SNCA 4 90626111 rs356182 3.89e-154 -0.2774 85: SPPL2B SPPL2B 19 2341047 rs55818311 4.18e-10 -0.0696 86: SPTSSB SPTSSB 3 161077630 rs1450522 5.01e-10 -0.0616 87: STK39 STK39 2 169110394 rs1474055 2.54e-39 0.1796 88: SYT17 SYT17 16 19277493 rs6497339 2.76e-11 0.0630 89: TMEM163 TMEM163 2 135464616 rs57891859 4.55e-14 0.0807 90: TMEM175 TMEM175 4 951947 rs34311866 9.98e-70 -0.2126 91: TRIM40 TRIM40 6 30108683 rs9261484 1.62e-08 -0.0635 92: UBAP2 UBAP2 9 34046391 rs6476434 6.58e-09 -0.0615 93: UBTF UBTF 17 42294337 rs2269906 6.24e-10 0.0631 94: VAMP4 VAMP4 1 171719769 rs11578699 4.47e-09 -0.0704 95: VPS13C VPS13C 15 61997385 rs2251086 6.08e-18 -0.1186 96: WNT3 WNT3 17 44866805 rs11658976 3.52e-08 -0.0624 97: ZNF608 ZNF608 5 124110273 rs6875262 1.02e-08 0.1141

3. Session info


> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS/LAPACK: /home/acarrasco/.conda/envs/echoverse/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] echolocatoR_2.0.1

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  reticulate_1.26
  [3] R.utils_2.12.0              tidyselect_1.1.2
  [5] RSQLite_2.2.17              AnnotationDbi_1.56.2
  [7] htmlwidgets_1.5.4           grid_4.1.2
  [9] BiocParallel_1.28.3         XGR_1.1.8
 [11] munsell_0.5.0               interp_1.1-3
 [13] DT_0.25                     colorspace_2.0-3
 [15] OrganismDbi_1.36.0          Biobase_2.54.0
 [17] filelock_1.0.2              knitr_1.40
 [19] supraHex_1.32.0             rstudioapi_0.14
 [21] stats4_4.1.2                DescTools_0.99.46
 [23] MatrixGenerics_1.6.0        GenomeInfoDbData_1.2.7
 [25] mixsqp_0.3-43               bit64_4.0.5
 [27] echoconda_0.99.7            basilisk_1.6.0
 [29] vctrs_0.4.1                 generics_0.1.3
 [31] xfun_0.33                   biovizBase_1.42.0
 [33] BiocFileCache_2.2.1         R6_2.5.1
 [35] GenomeInfoDb_1.30.1         AnnotationFilter_1.18.0
 [37] bitops_1.0-7                cachem_1.0.6
 [39] reshape_0.8.9               DelayedArray_0.20.0
 [41] assertthat_0.2.1            BiocIO_1.4.0
 [43] scales_1.2.1                nnet_7.3-17
 [45] rootSolve_1.8.2.3           gtable_0.3.1
 [47] lmom_2.9                    ggbio_1.42.0
 [49] ensembldb_2.18.4            rlang_1.0.5
 [51] echodata_0.99.12            splines_4.1.2
 [53] lazyeval_0.2.2              rtracklayer_1.54.0
 [55] dichromat_2.0-0.1           hexbin_1.28.2
 [57] checkmate_2.1.0             BiocManager_1.30.18
 [59] yaml_2.3.5                  reshape2_1.4.4
 [61] snpStats_1.44.0             backports_1.4.1
 [63] GenomicFeatures_1.46.5      ggnetwork_0.5.10
 [65] Hmisc_4.7-1                 RBGL_1.70.0
 [67] tools_4.1.2                 echoplot_0.99.5
 [69] ggplot2_3.3.6               ellipsis_0.3.2
 [71] catalogueR_1.0.0            RColorBrewer_1.1-3
 [73] proxy_0.4-27                BiocGenerics_0.40.0
 [75] coloc_5.2.0                 Rcpp_1.0.9
 [77] plyr_1.8.7                  base64enc_0.1-3
 [79] progress_1.2.2              zlibbioc_1.40.0
 [81] purrr_0.3.4                 RCurl_1.98-1.8
 [83] basilisk.utils_1.6.0        prettyunits_1.1.1
 [85] rpart_4.1.16                deldir_1.0-6
 [87] viridis_0.6.2               S4Vectors_0.32.4
 [89] SummarizedExperiment_1.24.0 ggrepel_0.9.1
 [91] cluster_2.1.2               fs_1.5.2
 [93] crul_1.3                    magrittr_2.0.3
 [95] data.table_1.14.2           echotabix_0.99.8
 [97] dnet_1.1.7                  openxlsx_4.2.5
 [99] mvtnorm_1.1-3               ProtGenerics_1.26.0
[101] matrixStats_0.62.0          hms_1.1.2
[103] patchwork_1.1.2             XML_3.99-0.10
[105] jpeg_0.1-9                  readxl_1.4.1
[107] IRanges_2.28.0              gridExtra_2.3
[109] compiler_4.1.2              biomaRt_2.50.3
[111] tibble_3.1.8                crayon_1.5.1
[113] R.oo_1.25.0                 htmltools_0.5.3
[115] echoannot_0.99.7            tzdb_0.3.0
[117] Formula_1.2-4               tidyr_1.2.1
[119] expm_0.999-6                Exact_3.1
[121] DBI_1.1.3                   dbplyr_2.2.1
[123] MASS_7.3-56                 rappdirs_0.3.3
[125] boot_1.3-28                 Matrix_1.4-1
[127] readr_2.1.2                 piggyback_0.1.4
[129] cli_3.4.0                   R.methodsS3_1.8.2
[131] echofinemap_0.99.3          parallel_4.1.2
[133] igraph_1.3.4                GenomicRanges_1.46.1
[135] pkgconfig_2.0.3             GenomicAlignments_1.30.0
[137] dir.expiry_1.2.0            RCircos_1.2.2
[139] foreign_0.8-82              osfr_0.2.8
[141] xml2_1.3.3                  XVector_0.34.0
[143] echoLD_0.99.7               stringr_1.4.1
[145] VariantAnnotation_1.40.0    digest_0.6.29
[147] graph_1.72.0                httpcode_0.3.0
[149] Biostrings_2.62.0           cellranger_1.1.0
[151] htmlTable_2.4.1             gld_2.6.5
[153] restfulr_0.0.15             curl_4.3.2
[155] Rsamtools_2.10.0            rjson_0.2.21
[157] lifecycle_1.0.2             nlme_3.1-157
[159] jsonlite_1.8.0              viridisLite_0.4.1
[161] BSgenome_1.62.0             fansi_1.0.3
[163] downloadR_0.99.4            pillar_1.8.1
[165] susieR_0.12.27              lattice_0.20-45
[167] GGally_2.1.2                KEGGREST_1.34.0
[169] fastmap_1.1.0               httr_1.4.4
[171] survival_3.3-1              glue_1.6.2
[173] zip_2.2.1                   png_0.1-7
[175] bit_4.0.4                   Rgraphviz_2.38.0
[177] class_7.3-20                stringi_1.7.8
[179] blob_1.2.3                  latticeExtra_0.6-30
[181] memoise_2.0.1               dplyr_1.0.10
[183] irlba_2.3.5                 e1071_1.7-11
[185] ape_5.6-2

Note First of all, the pipeline works as expected in the docker container. I also tried this. The echoverse conda environment was created last April, so it may well be this is an issue you already fixed. However, I also want to mention that when I ran it on my HPC using the default echoR_mini, the environment failed to be created

> res <- echolocatoR::finemap_loci(
  fullSS_path = fullSS_path,
  topSNPs = topSNPs,
  loci = c("BST1","MEX3C"),
  finemap_methods = c("ABF","FINEMAP","SUSIE"),
  dataset_name = "Nalls23andMe_2019",
  fullSS_genome_build = "hg19",
  bp_distance = 10000,
  munged = TRUE)
┌────────────────────────────────────────┐
│                                        │
│   )))> 🦇 BST1 [locus 1 / 2] 🦇 <(((   │
│                                        │
└────────────────────────────────────────┘

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Step 1 ▶▶▶ Query 🔎 ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────+ Query Method: tabix
Constructing GRanges query using min/max ranges within a single chromosome.
query_dat is already a GRanges object. Returning directly.
========= echotabix::convert =========
Converting full summary stats file to tabix format for fast querying.
Inferred format: 'table'
Explicit format: 'table'
Inferring comment_char from tabular header: 'SNP'
Determining chrom type from file header.
Assuming fullSS_path summary stats have already been processed with MungeSumstats.
Chromosome format: 1
Detecting column delimiter.
Identified column separator: \t
Sorting rows by coordinates via bash.
Searching for header row with grep.
( grep ^'SNP' .../nalls2019.fullSS_subset.tsv; grep
    -v ^'SNP' .../nalls2019.fullSS_subset.tsv | sort
    -k2,2n
    -k3,3n ) > .../file31ef0618927d70_sorted.tsv
Constructing outputs
Selecting valid alternative method: conda
bgzipping file with conda.
echoconda:: conda already installed.
Identified yaml file stored in echoconda.
Retrieving conda env name from yaml: /home/acarrasco/.conda/envs/echoverse/lib/R/library/echoconda/conda/echoR_mini.yml
Warning: Could not identify any conda_env matching existing conda environments.
echoconda:: Creating conda environment: echoR_mini
sh: 4: /home/acarrasco/.conda/envs/echoverse/etc/conda/deactivate.d/deactivate-r-base.sh: [[: not found
+ '/home/acarrasco/.cache/R/basilisk/1.6.0/0/bin/conda' 'create' '--yes' '--prefix' '/home/acarrasco/.cache/R/basilisk/1.6.0/echoconda/0.99.7/echoR_mini' 'python=3' '--quiet' '-c' 'conda-forge' '-c' 'bioconda' '-c' 'nodefaults'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/acarrasco/.cache/R/basilisk/1.6.0/echoconda/0.99.7/echoR_mini

  added / updated specs:
    - python=3

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.9.14  |       ha878542_0         152 KB  conda-forge
    libzlib-1.2.12             |       h166bdaf_3          65 KB  conda-forge
    openssl-3.0.5              |       h166bdaf_2         2.8 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.0 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  ca-certificates    conda-forge/linux-64::ca-certificates-2022.9.14-ha878542_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-12.1.0-h8d9b700_16
  libgomp            conda-forge/linux-64::libgomp-12.1.0-h8d9b700_16
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libsqlite          conda-forge/linux-64::libsqlite-3.39.3-h753d276_0
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
  libzlib            conda-forge/linux-64::libzlib-1.2.12-h166bdaf_3
  ncurses            conda-forge/linux-64::ncurses-6.3-h27087fc_1
  openssl            conda-forge/linux-64::openssl-3.0.5-h166bdaf_2
  pip                conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.10.6-ha86cf86_0_cpython
  readline           conda-forge/linux-64::readline-8.1.2-h0f457ee_0
  setuptools         conda-forge/noarch::setuptools-65.3.0-pyhd8ed1ab_1
  tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0
  tzdata             conda-forge/noarch::tzdata-2022c-h191b570_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/acarrasco/.cache/R/basilisk/1.6.0/0/bin/conda' 'install' '--yes' '--prefix' '/home/acarrasco/.cache/R/basilisk/1.6.0/echoconda/0.99.7/echoR_mini' 'python=3'
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base -c defaults conda

# All requested packages already installed.

+ '/home/acarrasco/.cache/R/basilisk/1.6.0/0/bin/conda' 'install' '--yes' '--prefix' '/home/acarrasco/.cache/R/basilisk/1.6.0/echoconda/0.99.7/echoR_mini' '-c' 'conda-forge' '-c' 'bioconda' '-c' 'nodefaults' 'python=3' 'axel=2' 'bitarray=2' 'fastparquet=0' 'gzip=1' 'htslib=1' 'networkx=2' 'pandas-plink=2' 'pip=22' 'pyarrow=7' 'python=3' 'requests=2' 'rpy2=3' 'scikit-learn=1' 'scipy=1' 'tabix=1' 'tqdm=4' 'wget=1'
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): \ | failed
bschilder commented 1 year ago

This is why:

conda_env = "echoverse"

This isn't the name of any conda env included in echoconda. So unless you already created this yourself previously, no such env exists and thus can't be used.

bschilder commented 1 year ago

Relates back to my question here: https://github.com/RajLabMSSM/echolocatoR/issues/87#issuecomment-1229281212

AMCalejandro commented 1 year ago

Echoverse does exist indeed. Please, see all the deps within the conda env

acarrasco@kronos:~$ conda list -n echoverse
# packages in environment at /home/acarrasco/.conda/envs/echoverse:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
abseil-cpp                20210324.2           h9c3ff4c_0    conda-forge
arrow-cpp                 7.0.0           py39h6409b3a_2_cpu    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
aws-c-cal                 0.5.11               h95a6274_0    conda-forge
aws-c-common              0.6.2                h7f98852_0    conda-forge
aws-c-event-stream        0.2.7               h3541f99_13    conda-forge
aws-c-io                  0.10.5               hfb6a706_0    conda-forge
aws-checksums             0.1.11               ha31a3da_7    conda-forge
aws-sdk-cpp               1.8.186              hb4091e7_3    conda-forge
axel                      2.17.11              h9b69904_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bcftools                  1.15                 h0ea216a_2    bioconda
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_9    conda-forge
bioconductor-annotationdbi 1.56.1            r41hdfd78af_0    bioconda
bioconductor-annotationfilter 1.18.0            r41hdfd78af_0    bioconda
bioconductor-biobase      2.54.0            r41h5c21468_1    bioconda
bioconductor-biocfilecache 2.2.0             r41hdfd78af_0    bioconda
bioconductor-biocgenerics 0.40.0            r41hdfd78af_0    bioconda
bioconductor-biocio       1.4.0             r41hdfd78af_0    bioconda
bioconductor-biocparallel 1.28.3            r41h619a076_0    bioconda
bioconductor-biomart      2.50.0            r41hdfd78af_0    bioconda
bioconductor-biostrings   2.62.0            r41h5c21468_1    bioconda
bioconductor-biovizbase   1.42.0            r41h5c21468_1    bioconda
bioconductor-bsgenome     1.62.0            r41hdfd78af_0    bioconda
bioconductor-delayedarray 0.20.0            r41h5c21468_1    bioconda
bioconductor-ensdb.hsapiens.v75 2.99.0           r41hdfd78af_11    bioconda
bioconductor-ensembldb    2.18.1            r41hdfd78af_0    bioconda
bioconductor-genomeinfodb 1.30.0            r41hdfd78af_0    bioconda
bioconductor-genomeinfodbdata 1.2.7             r41hdfd78af_1    bioconda
bioconductor-genomicalignments 1.30.0            r41h5c21468_1    bioconda
bioconductor-genomicfeatures 1.46.1            r41hdfd78af_0    bioconda
bioconductor-genomicranges 1.46.1            r41h5c21468_0    bioconda
bioconductor-ggbio        1.42.0            r41hdfd78af_0    bioconda
bioconductor-graph        1.72.0            r41h5c21468_1    bioconda
bioconductor-iranges      2.28.0            r41h5c21468_1    bioconda
bioconductor-keggrest     1.34.0            r41hdfd78af_0    bioconda
bioconductor-matrixgenerics 1.6.0             r41hdfd78af_0    bioconda
bioconductor-organismdbi  1.36.0            r41hdfd78af_0    bioconda
bioconductor-protgenerics 1.26.0            r41hdfd78af_0    bioconda
bioconductor-rbgl         1.70.0            r41h619a076_1    bioconda
bioconductor-rhtslib      1.26.0            r41h5c21468_1    bioconda
bioconductor-rsamtools    2.10.0            r41h619a076_1    bioconda
bioconductor-rtracklayer  1.54.0            r41hdc01c10_2    bioconda
bioconductor-s4vectors    0.32.3            r41h5c21468_0    bioconda
bioconductor-snpstats     1.44.0            r41h5c21468_1    bioconda
bioconductor-summarizedexperiment 1.24.0            r41hdfd78af_0    bioconda
bioconductor-variantannotation 1.40.0            r41h5c21468_1    bioconda
bioconductor-xvector      0.34.0            r41h5c21468_1    bioconda
bioconductor-zlibbioc     1.40.0            r41h5c21468_1    bioconda
bitarray                  2.4.0            py39hb9d737c_0    conda-forge
bokeh                     2.4.2            py39hf3d152e_0    conda-forge
brotli                    1.0.9                h7f98852_6    conda-forge
brotli-bin                1.0.9                h7f98852_6    conda-forge
brotlipy                  0.7.0           py39h3811e60_1003    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           2021.10.8            ha878542_0    conda-forge
cairo                     1.16.0            ha12eb4b_1010    conda-forge
certifi                   2021.10.8        py39hf3d152e_1    conda-forge
cffi                      1.15.0           py39h4bc2ebd_0    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
click                     8.0.4            py39hf3d152e_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
cramjam                   2.5.0            py39h860a657_0    conda-forge
cryptography              36.0.2           py39hd97740a_0    conda-forge
curl                      7.82.0               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.11.2           py39h3811e60_1    conda-forge
dask                      2022.3.0           pyhd8ed1ab_0    conda-forge
dask-core                 2022.3.0           pyhd8ed1ab_0    conda-forge
deprecated                1.2.13             pyh6c4a22f_0    conda-forge
distributed               2022.3.0           pyhd8ed1ab_0    conda-forge
expat                     2.4.7                h27087fc_0    conda-forge
fastparquet               0.8.0            py39hce5d2b2_1    conda-forge
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                2.13.96              h8e229c2_2    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.31.2           py39hb9d737c_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
fsspec                    2022.2.0           pyhd8ed1ab_0    conda-forge
gcc_impl_linux-64         9.4.0               h03d3576_14    conda-forge
gcc_linux-64              9.4.0                h391b98a_9    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
gfortran_impl_linux-64    9.4.0               h0003116_14    conda-forge
gfortran_linux-64         9.4.0                hf0ab688_9    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glog                      0.5.0                h48cff8f_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
grpc-cpp                  1.43.2               h9e046d8_1    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gxx_impl_linux-64         9.4.0               h03d3576_14    conda-forge
gxx_linux-64              9.4.0                h0316aca_9    conda-forge
harfbuzz                  3.4.0                hb4a5f5f_0    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
htslib                    1.15                 h9753748_0    bioconda
icu                       69.1                 h9c3ff4c_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.3           py39hf3d152e_0    conda-forge
importlib_metadata        4.11.3               hd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jinja2                    3.1.1              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.0            py39hf939315_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_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           13_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_6    conda-forge
libbrotlidec              1.0.9                h7f98852_6    conda-forge
libbrotlienc              1.0.9                h7f98852_6    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   7.82.0               h7bff187_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
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     9.4.0               hd854feb_14    conda-forge
libgcc-ng                 11.2.0              h1d223b6_14    conda-forge
libgfortran-ng            11.2.0              h69a702a_14    conda-forge
libgfortran5              11.2.0              h5c6108e_14    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   11.2.0              h1d223b6_14    conda-forge
libgoogle-cloud           1.35.0               h6945097_2    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libidn2                   2.3.2                h7f98852_0    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libprotobuf               3.19.4               h780b84a_0    conda-forge
libsanitizer              9.4.0               h79bfe98_14    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-devel_linux-64  9.4.0               hd854feb_14    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_14    conda-forge
libthrift                 0.15.0               he6d91bd_1    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libutf8proc               2.7.0                h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.9.12               h885dcf4_1    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
locket                    0.2.0                      py_2    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                2.1.1            py39hb9d737c_0    conda-forge
matplotlib-base           3.5.1            py39h2fa2bec_0    conda-forge
msgpack-python            1.0.3            py39h1a9c180_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h9c3ff4c_0    conda-forge
networkx                  2.7.1              pyhd8ed1ab_1    conda-forge
numpy                     1.22.3           py39h18676bf_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1n               h166bdaf_0    conda-forge
orc                       1.7.3                h1be678f_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.1            py39hde0f152_0    conda-forge
pandas-plink              2.2.9            py39h3811e60_0    conda-forge
pango                     1.48.10              h4dcc4a0_3    conda-forge
parquet-cpp               1.5.1                         2    conda-forge
partd                     1.2.0              pyhd8ed1ab_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
pillow                    9.0.1            py39hae2aec6_2    conda-forge
pip                       22.0.4             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
plink                     1.90b6.21            hec16e2b_2    bioconda
pluggy                    1.0.0            py39hf3d152e_2    conda-forge
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
prompt_toolkit            3.0.27               hd8ed1ab_0    conda-forge
psutil                    5.9.0            py39h3811e60_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
pyarrow                   7.0.0           py39hff6fa39_2_cpu    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_4    conda-forge
pytest                    7.1.1            py39hf3d152e_0    conda-forge
python                    3.9.12          h9a8a25e_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2022.1             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pytz-deprecation-shim     0.1.0.post0      py39hf3d152e_1    conda-forge
pyyaml                    6.0              py39h3811e60_3    conda-forge
r                         4.1             r41hd8ed1ab_1004    conda-forge
r-acepack                 1.4.1           r41h859d828_1006    conda-forge
r-askpass                 1.1               r41hcfec24a_2    conda-forge
r-assertthat              0.2.1             r41hc72bb7e_2    conda-forge
r-backports               1.4.1             r41hcfec24a_0    conda-forge
r-base                    4.1.2                hde4fec0_0    conda-forge
r-base64enc               0.1_3           r41hcfec24a_1004    conda-forge
r-bh                      1.78.0_0          r41hc72bb7e_0    conda-forge
r-biocmanager             1.30.16           r41hc72bb7e_0    conda-forge
r-bit                     4.0.4             r41hcfec24a_0    conda-forge
r-bit64                   4.0.5             r41hcfec24a_0    conda-forge
r-bitops                  1.0_7             r41hcfec24a_0    conda-forge
r-blob                    1.2.2             r41hc72bb7e_0    conda-forge
r-boot                    1.3_28            r41hc72bb7e_0    conda-forge
r-brio                    1.1.3             r41hcfec24a_0    conda-forge
r-cachem                  1.0.6             r41hcfec24a_0    conda-forge
r-callr                   3.7.0             r41hc72bb7e_0    conda-forge
r-checkmate               2.0.0             r41hcfec24a_1    conda-forge
r-class                   7.3_20            r41hcfec24a_0    conda-forge
r-cli                     3.2.0             r41h03ef668_0    conda-forge
r-cluster                 2.1.2             r41h859d828_0    conda-forge
r-codetools               0.2_18            r41hc72bb7e_0    conda-forge
r-colorspace              2.0_3             r41h06615bd_0    conda-forge
r-crayon                  1.5.1             r41hc72bb7e_0    conda-forge
r-curl                    4.3.2             r41hcfec24a_0    conda-forge
r-data.table              1.14.2            r41hcfec24a_0    conda-forge
r-dbi                     1.1.2             r41hc72bb7e_0    conda-forge
r-dbplyr                  2.1.1             r41hc72bb7e_0    conda-forge
r-desc                    1.4.1             r41hc72bb7e_0    conda-forge
r-dichromat               2.0_0           r41ha770c72_2002    conda-forge
r-diffobj                 0.3.5             r41hcfec24a_0    conda-forge
r-digest                  0.6.29            r41h03ef668_0    conda-forge
r-dplyr                   1.0.8             r41h7525677_0    conda-forge
r-ellipsis                0.3.2             r41hcfec24a_0    conda-forge
r-evaluate                0.15              r41hc72bb7e_0    conda-forge
r-fansi                   1.0.3             r41h06615bd_0    conda-forge
r-farver                  2.1.0             r41h03ef668_0    conda-forge
r-fastmap                 1.1.0             r41h03ef668_0    conda-forge
r-filelock                1.0.2           r41hcfec24a_1002    conda-forge
r-forcats                 0.5.1             r41hc72bb7e_0    conda-forge
r-foreign                 0.8_82            r41hcfec24a_0    conda-forge
r-formatr                 1.11              r41hc72bb7e_0    conda-forge
r-formula                 1.2_4             r41hc72bb7e_0    conda-forge
r-futile.logger           1.4.3           r41hc72bb7e_1003    conda-forge
r-futile.options          1.0.1           r41hc72bb7e_1002    conda-forge
r-generics                0.1.2             r41hc72bb7e_0    conda-forge
r-ggally                  2.1.2             r41hc72bb7e_0    conda-forge
r-ggplot2                 3.3.5             r41hc72bb7e_0    conda-forge
r-glue                    1.6.2             r41h06615bd_0    conda-forge
r-gridextra               2.3             r41hc72bb7e_1003    conda-forge
r-gtable                  0.3.0             r41hc72bb7e_3    conda-forge
r-highr                   0.9               r41hc72bb7e_0    conda-forge
r-hmisc                   4.6_0             r41h859d828_0    conda-forge
r-hms                     1.1.1             r41hc72bb7e_0    conda-forge
r-htmltable               2.4.0             r41hc72bb7e_0    conda-forge
r-htmltools               0.5.2             r41h03ef668_0    conda-forge
r-htmlwidgets             1.5.4             r41hc72bb7e_0    conda-forge
r-httr                    1.4.2             r41hc72bb7e_0    conda-forge
r-isoband                 0.2.5             r41h03ef668_0    conda-forge
r-jpeg                    0.1_9             r41hcfec24a_0    conda-forge
r-jsonlite                1.8.0             r41h06615bd_0    conda-forge
r-kernsmooth              2.23_20           r41h742201e_0    conda-forge
r-knitr                   1.38              r41hc72bb7e_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_1    conda-forge
r-lambda.r                1.2.4             r41hc72bb7e_1    conda-forge
r-lattice                 0.20_45           r41hcfec24a_0    conda-forge
r-latticeextra            0.6_29            r41hc72bb7e_1    conda-forge
r-lazyeval                0.2.2             r41hcfec24a_2    conda-forge
r-lifecycle               1.0.1             r41hc72bb7e_0    conda-forge
r-magrittr                2.0.2             r41hcfec24a_0    conda-forge
r-mass                    7.3_56            r41h06615bd_0    conda-forge
r-matrix                  1.4_1             r41h0154571_0    conda-forge
r-matrixstats             0.61.0            r41hcfec24a_0    conda-forge
r-memoise                 2.0.1             r41hc72bb7e_0    conda-forge
r-mgcv                    1.8_39            r41h0154571_0    conda-forge
r-mime                    0.12              r41hcfec24a_0    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1004    conda-forge
r-nlme                    3.1_157           r41h8da6f51_0    conda-forge
r-nnet                    7.3_17            r41hcfec24a_0    conda-forge
r-openssl                 2.0.0             r41hfaab4ff_0    conda-forge
r-pillar                  1.7.0             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_1    conda-forge
r-pkgload                 1.2.4             r41h03ef668_0    conda-forge
r-plogr                   0.2.0           r41hc72bb7e_1003    conda-forge
r-plyr                    1.8.7             r41h7525677_0    conda-forge
r-png                     0.1_7           r41hcfec24a_1004    conda-forge
r-praise                  1.0.0           r41hc72bb7e_1005    conda-forge
r-prettyunits             1.1.1             r41hc72bb7e_1    conda-forge
r-processx                3.5.3             r41h06615bd_0    conda-forge
r-progress                1.2.2             r41hc72bb7e_2    conda-forge
r-ps                      1.6.0             r41hcfec24a_0    conda-forge
r-purrr                   0.3.4             r41hcfec24a_1    conda-forge
r-r6                      2.5.1             r41hc72bb7e_0    conda-forge
r-rappdirs                0.3.3             r41hcfec24a_0    conda-forge
r-rcolorbrewer            1.1_2           r41h785f33e_1003    conda-forge
r-rcpp                    1.0.8.3           r41h7525677_0    conda-forge
r-rcurl                   1.98_1.6          r41hcfec24a_0    conda-forge
r-recommended             4.1             r41hd8ed1ab_1004    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_1    conda-forge
r-reshape                 0.8.8             r41hc72bb7e_3    conda-forge
r-reshape2                1.4.4             r41h03ef668_1    conda-forge
r-restfulr                0.0.13            r41h73dbb54_2    bioconda
r-rjson                   0.2.21            r41h03ef668_0    conda-forge
r-rlang                   1.0.2             r41h7525677_0    conda-forge
r-rpart                   4.1.16            r41hcfec24a_0    conda-forge
r-rprojroot               2.0.2             r41hc72bb7e_0    conda-forge
r-rsqlite                 2.2.8             r41h03ef668_0    conda-forge
r-rstudioapi              0.13              r41hc72bb7e_0    conda-forge
r-scales                  1.1.1             r41hc72bb7e_0    conda-forge
r-snow                    0.4_4             r41hc72bb7e_0    conda-forge
r-spatial                 7.3_15            r41hcfec24a_0    conda-forge
r-stringi                 1.7.6             r41h337692f_1    conda-forge
r-stringr                 1.4.0             r41hc72bb7e_2    conda-forge
r-survival                3.3_1             r41h06615bd_0    conda-forge
r-sys                     3.4               r41hcfec24a_0    conda-forge
r-testthat                3.1.2             r41h03ef668_0    conda-forge
r-tibble                  3.1.6             r41hcfec24a_0    conda-forge
r-tidyr                   1.2.0             r41h03ef668_0    conda-forge
r-tidyselect              1.1.2             r41hc72bb7e_0    conda-forge
r-utf8                    1.2.2             r41hcfec24a_0    conda-forge
r-vctrs                   0.3.8             r41hcfec24a_1    conda-forge
r-viridis                 0.6.2             r41hc72bb7e_0    conda-forge
r-viridislite             0.4.0             r41hc72bb7e_0    conda-forge
r-waldo                   0.4.0             r41hc72bb7e_0    conda-forge
r-withr                   2.5.0             r41hc72bb7e_0    conda-forge
r-xfun                    0.30              r41h7525677_0    conda-forge
r-xml                     3.99_0.9          r41h06615bd_0    conda-forge
r-xml2                    1.3.3             r41h03ef668_0    conda-forge
r-yaml                    2.3.5             r41h06615bd_0    conda-forge
radian                    0.6.0              pyhd8ed1ab_0    conda-forge
rchitect                  0.3.36           py39hb9d737c_0    conda-forge
re2                       2022.02.01           h9c3ff4c_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
rpy2                      3.4.5           py39r41hce5d2b2_3    conda-forge
s2n                       1.0.10               h9b69904_0    conda-forge
scikit-learn              1.0.2            py39h4dfa638_0    conda-forge
scipy                     1.8.0            py39hee8e79c_1    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
setuptools                61.2.0           py39hf3d152e_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.8                he1b5a44_3    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
sqlite                    3.37.1               h4ff8645_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.11.2             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h3811e60_2    conda-forge
tqdm                      4.63.1             pyhd8ed1ab_0    conda-forge
typing_extensions         4.1.1              pyha770c72_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
tzlocal                   4.1              py39hf3d152e_1    conda-forge
unicodedata2              14.0.0           py39h3811e60_0    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
wrapt                     1.14.0           py39hb9d737c_0    conda-forge
xarray                    2022.3.0           pyhd8ed1ab_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
yaml                      0.2.5                h7f98852_2    conda-forge
zict                      2.1.0              pyhd8ed1ab_0    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstandard                 0.17.0           py39h3811e60_0    conda-forge
zstd                      1.5.2                ha95c52
AMCalejandro commented 1 year ago

I believe I tried to use my conda environment ( created last May I believe), because the echoR_mini was failing to load in my HPC

bschilder commented 1 year ago

You might want to give echoR_mini another try since I've made quite a few changes to echoconda since then.

In the meantime, I'll try reproducing this error with the yaml you provided here: https://github.com/RajLabMSSM/echolocatoR/issues/87#issuecomment-1252397139

bschilder commented 1 year ago

The "echoverse" conda env you supplied here seems to build for me:

echoverse.yml.txt

wget https://github.com/RajLabMSSM/echolocatoR/files/9893718/echoverse.yml.txt
conda env create -f echoverse.yml.txt

However, I would still recommend you use the default "echoR_mini" env as this is specifically designed for the latest version of echolocatoR, and is installed automatically.