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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
994 stars 354 forks source link

library(tidyverse) : there is no package called ‘tidyverse’ #3445

Closed tykim0109 closed 3 years ago

tykim0109 commented 3 years ago

Version info

To Reproduce Exact bcbio command you have used:

bcbio_nextgen.py ../config/K0008-K0011_RNA_updated.yaml -n 96

Your sample configuration file:

details:
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0006-BF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/S1N7CLEQE-23022021_S10_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/S1N7CLEQE-23022021_S10_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0006-BF1
    phenotype: tumor
    validate_batch: group0
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0011-BF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/S6TRHC9B1-23022021_S16_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/S6TRHC9B1-23022021_S16_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0011-BF1
    phenotype: tumor
    validate_batch: group4
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0011-AF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SK6762KAZ-23022021_S15_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SK6762KAZ-23022021_S15_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0011-AF1
    phenotype: tumor
    validate_batch: group4
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0009-AF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SM30WC7P9-23022021_S13_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SM30WC7P9-23022021_S13_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0009-AF1
    phenotype: tumor
    validate_batch: group2
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0008-AF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SM8EGVGWJ-23022021_S12_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SM8EGVGWJ-23022021_S12_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0008-AF1
    phenotype: tumor
    validate_batch: group1
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0006-AF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SQS2JA66K-23022021_S9_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SQS2JA66K-23022021_S9_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0006-AF1
    phenotype: tumor
    validate_batch: group0
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0008-AF1-LMDRNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SSRGQRVBA-23022021_S11_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SSRGQRVBA-23022021_S11_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0008-AF1-LMD
    phenotype: tumor
    validate_batch: group1
- algorithm:
    aligner: star
    fusion_caller:
    - pizzly
    - oncofuse
    - arriba
    hlacaller: optitype
    strandedness: firststrand
    variantcaller:
    - gatk-haplotype
  analysis: RNA-seq
  description: K0010-AF1-RNAseq
  files:
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SSRIVPS0A-23022021_S14_R1_001.fastq.gz
  - /apps2/data/K008-K0011_Target_Discovery/input/RNA/SSRIVPS0A-23022021_S14_R2_001.fastq.gz
  genome_build: hg38
  metadata:
    batch: K0010-AF1
    phenotype: tumor
    validate_batch: group3
fc_name: K0008-K0011_RNA
upload:
  dir: ../final

Observed behavior Error message or bcbio output:

Traceback (most recent call last):
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/apps1/local/share/bcbio/anaconda/envs/r36/bin/Rscript --vanilla -e library(tidyverse);salmon_files = list.files("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/salmon", pattern="quant.sf", recursive=TRUE, full.names=TRUE);tx2gene = readr::read_csv("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/inputs/transcriptome/tx2gene.csv", col_names=c("transcript", "gene")); samples = basename(dirname(salmon_files));names(salmon_files) = samples;txi = tximport::tximport(salmon_files, type="salmon", tx2gene=tx2gene, countsFromAbundance="lengthScaledTPM", dropInfReps=TRUE);readr::write_csv(round(txi$counts) %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmpyh6_tqvc/tximport-counts.csv");readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmp9mjt2ip1/tximport-tpm.csv");
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/apps1/local/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/apps1/local/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 264, in rnaseqpipeline
    samples = rnaseq.combine_files(samples)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/rnaseq.py", line 489, in combine_files
    tximport = load_tximport(data)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/rnaseq.py", line 556, in load_tximport
    do.run([rcmd, "--vanilla", "-e", render_string], f"Loading tximport.")
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/apps1/local/share/bcbio/anaconda/envs/r36/bin/Rscript --vanilla -e library(tidyverse);salmon_files = list.files("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/salmon", pattern="quant.sf", recursive=TRUE, full.names=TRUE);tx2gene = readr::read_csv("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/inputs/transcriptome/tx2gene.csv", col_names=c("transcript", "gene")); samples = basename(dirname(salmon_files));names(salmon_files) = samples;txi = tximport::tximport(salmon_files, type="salmon", tx2gene=tx2gene, countsFromAbundance="lengthScaledTPM", dropInfReps=TRUE);readr::write_csv(round(txi$counts) %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmpyh6_tqvc/tximport-counts.csv");readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmp9mjt2ip1/tximport-tpm.csv");
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
' returned non-zero exit status 1.

Expected behavior A clear and concise description of what you expected to happen.

Log files Please attach (10MB max): bcbio-nextgen.log, bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log. bcbio-nextgen.log bcbio-nextgen-debug.log bcbio-nextgen-commands.log

Additional context Add any other context about the problem here. bulkRNA-seq pipeline failed with error in 'library(tidyverse)'. I tried to install tidyverse with conda forge or install.packages("tidyverse"). It seemed to install tidyverse successfully (See below):

trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
==================================================
downloaded 696 KB

* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tidyverse)

The downloaded source packages are in
        ‘/tmp/RtmpG0JxxC/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

But, I can't load tidyverse package even after successful installation of tidyverse. 

library(tidyverse)
Error: package or namespace load failed for ‘tidyverse’:
.onAttach failed in attachNamespace() for 'tidyverse', details:
call: clienv$num_colors[[std]]
error: subscript out of bounds

Could you tell me how to fix this issue? How can I install and load tidyverse? Thank you.

naumenko-sa commented 3 years ago

Hi @tykim0109 !

Thanks for reporting and sorry about the issues. We install tidyverse via conda: https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml#L274

Is there any chance that you have upgraded from the old version but you have not upgraded tools?

bcbio_nextgen.py upgrade -u skip --tools

Or directly in conda (install in r36 environment, not in base)

conda install -n r36 -c conda-forge r-tidyverse

It is better to upgrade tools since there could be other packages missing.

Sergey

tykim0109 commented 3 years ago

Thank you @naumenko-sa for your kind help. I upgraded successfully by 'bcbio_nextgen.py upgrade -u skip --tools'. But, it's still not working. Please see below.

Upgrading bcbio
Upgrading third party tools to latest versions
Reading packages from /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/tmpbcbio-install/cloudbiolinux/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
Checking for problematic or migrated packages in default environment
# Installing into conda environment default: age-metasv, arriba, bamtools=2.4.0, bamutil, bbmap, bcbio-prioritize, bcbio-variation, bcbio-variation-recall, bcftools, bedops, bedtools, bio-vcf, biobambam, bowtie, bowtie2, break-point-inspector, bwa, cage, cancerit-allelecount, chipseq-greylist, cnvkit, coincbc, cramtools, cufflinks, cyvcf2, deeptools, delly, duphold, ensembl-vep=100.*, express, extract-sv-reads, fastp, fastqc>=0.11.8=1, fgbio, freebayes, gatk, gatk4, geneimpacts, genesplicer, gffcompare, goleft, grabix, gridss, gsort, gvcfgenotyper, h5py, hisat2, hmftools-amber, hmftools-cobalt, hmftools-purple, hmmlearn, hts-nim-tools, htslib, impute2, kallisto>=0.43.1, kraken, ldc>=1.13.0, lofreq, macs2, maxentscan, mbuffer, minimap2, mintmap, mirdeep2=2.0.0.7, mirtop, moreutils, multiqc, multiqc-bcbio, ngs-disambiguate, novoalign, octopus>=0.5.1b, oncofuse, optitype>=1.3.4, pandoc=2.9.2, parallel, pbgzip, peddy, perl-sanger-cgp-battenberg, picard, pindel, pizzly, pyloh, pysam>=0.14.0, pythonpy, qsignature, qualimap, rapmap, razers3=3.5.0, rtg-tools, sailfish, salmon, sambamba, samblaster, samtools=1.9, scalpel, seq2c<2016, seqbuster, seqcluster, seqtk, sickle-trim, simple_sv_annotation, singlecell-barcodes, snap-aligner=1.0dev.97, snpeff=4.3.1t, solvebio, spades, staden_io_lib, star=2.6.1d, stringtie, subread, survivor, tdrmapper, tophat-recondition, trim-galore, ucsc-bedgraphtobigwig, ucsc-bedtobigbed, ucsc-bigbedinfo, ucsc-bigbedsummary, ucsc-bigbedtobed, ucsc-bigwiginfo, ucsc-bigwigsummary, ucsc-bigwigtobedgraph, ucsc-bigwigtowig, ucsc-fatotwobit, ucsc-gtftogenepred, ucsc-liftover, ucsc-wigtobigwig, umis, vardict-java, vardict<=2015, variantbam, varscan, vcfanno, vcflib, verifybamid2, viennarna, vqsr_cnn, vt, wham, anaconda-client, awscli, bzip2, ncurses, nodejs, p7zip, readline, s3gof3r, xz, perl-app-cpanminus, perl-archive-extract, perl-archive-zip, perl-bio-db-sam, perl-cgi, perl-dbi, perl-encode-locale, perl-file-fetch, perl-file-sharedir, perl-file-sharedir-install, perl-ipc-system-simple, perl-lwp-protocol-https, perl-lwp-simple, perl-statistics-descriptive, perl-time-hires, perl-vcftools-vcf, bioconductor-annotate, bioconductor-apeglm, bioconductor-biocgenerics, bioconductor-biocinstaller, bioconductor-biocstyle, bioconductor-biostrings, bioconductor-biovizbase, bioconductor-bsgenome.hsapiens.ucsc.hg19, bioconductor-bsgenome.hsapiens.ucsc.hg38, bioconductor-bubbletree, bioconductor-cn.mops, bioconductor-copynumber, bioconductor-degreport, bioconductor-deseq2, bioconductor-dexseq, bioconductor-dnacopy, bioconductor-genomeinfodbdata, bioconductor-genomicranges, bioconductor-iranges, bioconductor-limma, bioconductor-rtracklayer, bioconductor-snpchip, bioconductor-titancna, bioconductor-vsn>=3.50.0, r-base, r-basejump=0.7.2, r-bcbiornaseq>=0.2.7, r-cghflasso, r-chbutils, r-devtools, r-dplyr, r-dt, r-ggdendro, r-ggplot2, r-ggrepel>=0.7, r-gplots, r-gsalib, r-janitor, r-knitr, r-pheatmap, r-plyr, r-pscbs, r-reshape, r-rmarkdown, r-rsqlite, r-sleuth, r-snow, r-stringi, r-viridis>=0.5, r-wasabi, r=3.5.1, xorg-libxt

## Package Plan ##

  environment location: /apps1/local/share/bcbio/anaconda

  added / updated specs:
    - age-metasv
    - anaconda-client
    - arriba
    - awscli
    - bamtools=2.4.0
    - bamutil
    - bbmap
    - bcbio-prioritize
    - bcbio-variation
    - bcbio-variation-recall
    - bcftools
    - bedops
    - bedtools
    - bio-vcf
    - biobambam
    - bioconductor-annotate
    - bioconductor-apeglm
    - bioconductor-biocgenerics
    - bioconductor-biocinstaller
    - bioconductor-biocstyle
    - bioconductor-biostrings
    - bioconductor-biovizbase
    - bioconductor-bsgenome.hsapiens.ucsc.hg19
    - bioconductor-bsgenome.hsapiens.ucsc.hg38
    - bioconductor-bubbletree
    - bioconductor-cn.mops
    - bioconductor-copynumber
    - bioconductor-degreport
    - bioconductor-deseq2
    - bioconductor-dexseq
    - bioconductor-dnacopy
    - bioconductor-genomeinfodbdata
    - bioconductor-genomicranges
    - bioconductor-iranges
    - bioconductor-limma
    - bioconductor-rtracklayer
    - bioconductor-snpchip
    - bioconductor-titancna
    - bioconductor-vsn[version='>=3.50.0']
    - bowtie
    - bowtie2
    - break-point-inspector
    - bwa
    - bzip2
    - cage
    - cancerit-allelecount
    - chipseq-greylist
    - cnvkit
    - coincbc
    - cramtools
    - cufflinks
    - cyvcf2
    - deeptools
    - delly
    - duphold
    - ensembl-vep=100
    - express
    - extract-sv-reads
    - fastp
    - fastqc[version='>=0.11.8',build=1]
    - fgbio
    - freebayes
    - gatk
    - gatk4
    - geneimpacts
    - genesplicer
    - gffcompare
    - goleft
    - grabix
    - gridss
    - gsort
    - gvcfgenotyper
    - h5py
    - hisat2
    - hmftools-amber
    - hmftools-cobalt
    - hmftools-purple
    - hmmlearn
    - hts-nim-tools
    - htslib
    - impute2
    - kallisto[version='>=0.43.1']
    - kraken
    - ldc[version='>=1.13.0']
    - lofreq
    - macs2
    - maxentscan
    - mbuffer
    - minimap2
    - mintmap
    - mirdeep2=2.0.0.7
    - mirtop
    - moreutils
    - multiqc
    - multiqc-bcbio
    - ncurses
    - ngs-disambiguate
    - nodejs
    - novoalign
    - octopus[version='>=0.5.1b']
    - oncofuse
    - optitype[version='>=1.3.4']
    - p7zip
    - pandoc=2.9.2
    - parallel
    - pbgzip
    - peddy
    - perl-app-cpanminus
    - perl-archive-extract
    - perl-archive-zip
    - perl-bio-db-sam
    - perl-cgi
    - perl-dbi
    - perl-encode-locale
    - perl-file-fetch
    - perl-file-sharedir
    - perl-file-sharedir-install
    - perl-ipc-system-simple
    - perl-lwp-protocol-https
    - perl-lwp-simple
    - perl-sanger-cgp-battenberg
    - perl-statistics-descriptive
    - perl-time-hires
    - perl-vcftools-vcf
    - picard
    - pindel
    - pizzly
    - pyloh
    - pysam[version='>=0.14.0']
    - python=3
    - pythonpy
    - qsignature
    - qualimap
    - r-base
    - r-basejump=0.7.2
    - r-bcbiornaseq[version='>=0.2.7']
    - r-cghflasso
    - r-chbutils
    - r-devtools
    - r-dplyr
    - r-dt
    - r-ggdendro
    - r-ggplot2
    - r-ggrepel[version='>=0.7']
    - r-gplots
    - r-gsalib
    - r-janitor
    - r-knitr
    - r-pheatmap
    - r-plyr
    - r-pscbs
    - r-reshape
    - r-rmarkdown
    - r-rsqlite
    - r-sleuth
    - r-snow
    - r-stringi
    - r-viridis[version='>=0.5']
    - r-wasabi
    - r=3.5.1
    - rapmap
    - razers3=3.5.0
    - readline
    - rtg-tools
    - s3gof3r
    - sailfish
    - salmon
    - sambamba
    - samblaster
    - samtools=1.9
    - scalpel
    - seq2c[version='<2016']
    - seqbuster
    - seqcluster
    - seqtk
    - sickle-trim
    - simple_sv_annotation
    - singlecell-barcodes
    - snap-aligner=1.0dev.97
    - snpeff=4.3.1t
    - solvebio
    - spades
    - staden_io_lib
    - star=2.6.1d
    - stringtie
    - subread
    - survivor
    - tdrmapper
    - tophat-recondition
    - trim-galore
    - ucsc-bedgraphtobigwig
    - ucsc-bedtobigbed
    - ucsc-bigbedinfo
    - ucsc-bigbedsummary
    - ucsc-bigbedtobed
    - ucsc-bigwiginfo
    - ucsc-bigwigsummary
    - ucsc-bigwigtobedgraph
    - ucsc-bigwigtowig
    - ucsc-fatotwobit
    - ucsc-gtftogenepred
    - ucsc-liftover
    - ucsc-wigtobigwig
    - umis
    - vardict-java
    - vardict[version='<=2015']
    - variantbam
    - varscan
    - vcfanno
    - vcflib
    - verifybamid2
    - viennarna
    - vqsr_cnn
    - vt
    - wham
    - xorg-libxt
    - xz

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    r-janitor-2.0.1            |    r35h6115d3f_0         235 KB  conda-forge
    r-snakecase-0.11.0         |    r35h6115d3f_1         175 KB  conda-forge
    vardict-1.8.2              |          pl526_0         102 KB  bioconda
    ------------------------------------------------------------
                                           Total:         513 KB

The following NEW packages will be INSTALLED:

  arriba             bioconda/linux-64::arriba-1.2.0-h248197f_1
  bioconductor-anno~ bioconda/noarch::bioconductor-annotationfilter-1.6.0-r351_0
  bioconductor-apeg~ bioconda/linux-64::bioconductor-apeglm-1.4.1-r351hf484d3e_0
  bioconductor-biov~ bioconda/linux-64::bioconductor-biovizbase-1.30.1-r351h14c3975_0
  bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome-1.50.0-r351_0
  bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome.hsapiens.ucsc.hg19-1.4.0-r351_5
  bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.1-r351_5
  bioconductor-bubb~ bioconda/linux-64::bioconductor-bubbletree-2.6.0-0
  bioconductor-cn.m~ bioconda/linux-64::bioconductor-cn.mops-1.28.0-r351hf484d3e_0
  bioconductor-copy~ bioconda/noarch::bioconductor-copynumber-1.22.0-r351_0
  bioconductor-degr~ bioconda/noarch::bioconductor-degreport-1.19.1-r351_0
  bioconductor-dese~ bioconda/linux-64::bioconductor-deseq2-1.22.1-r351hf484d3e_0
  bioconductor-dexs~ bioconda/noarch::bioconductor-dexseq-1.28.0-r351_0
  bioconductor-ense~ bioconda/noarch::bioconductor-ensembldb-2.6.3-r351_0
  bioconductor-exom~ bioconda/linux-64::bioconductor-exomecopy-1.28.0-r351h14c3975_0
  bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.18.1-r351_0
  bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.1-r351_0
  bioconductor-geno~ bioconda/linux-64::bioconductor-genomicalignments-1.18.1-r351h14c3975_0
  bioconductor-geno~ bioconda/noarch::bioconductor-genomicfeatures-1.34.1-r351_0
  bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.34.0-r351h14c3975_0
  bioconductor-olig~ bioconda/noarch::bioconductor-oligoclasses-1.44.0-r351_0
  bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-1.34.0-r351hf484d3e_0
  bioconductor-rtra~ bioconda/linux-64::bioconductor-rtracklayer-1.42.1-r351h9d9f1b6_1
  bioconductor-snpc~ bioconda/noarch::bioconductor-snpchip-2.28.0-r351_0
  bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.12.0-r351_0
  bioconductor-tita~ bioconda/linux-64::bioconductor-titancna-1.20.1-r351h14c3975_0
  bioconductor-txim~ bioconda/noarch::bioconductor-tximport-1.12.1-r351_1
  bioconductor-vari~ bioconda/linux-64::bioconductor-variantannotation-1.28.3-r351h14c3975_0
  hmftools-amber     bioconda/noarch::hmftools-amber-3.5-0
  hmftools-cobalt    bioconda/noarch::hmftools-cobalt-1.11-0
  hmftools-purple    bioconda/noarch::hmftools-purple-2.52-0
  qualimap           bioconda/noarch::qualimap-2.2.2d-1
  r-basejump         bioconda/linux-64::r-basejump-0.7.2-r351_1
  r-bcbiobase        bioconda/linux-64::r-bcbiobase-0.4.1-r351_3
  r-bcbiornaseq      bioconda/linux-64::r-bcbiornaseq-0.2.9-r351_0
  r-janitor          conda-forge/noarch::r-janitor-2.0.1-r35h6115d3f_0
  r-optparse         conda-forge/noarch::r-optparse-1.6.6-r35h6115d3f_0
  r-pscbs            bioconda/linux-64::r-pscbs-0.65.0-r351h6115d3f_0
  r-snakecase        conda-forge/noarch::r-snakecase-0.11.0-r35h6115d3f_1
  r-tidyverse        conda-forge/noarch::r-tidyverse-1.3.0-r35h6115d3f_1

The following packages will be DOWNGRADED:

  pandoc                                  2.10.1-h516909a_0 --> 2.9.2.1-0
  vardict                                2019.06.04-pl526_0 --> 1.8.2-pl526_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment bwakit: bwakit

## Package Plan ##

  environment location: /apps1/local/share/bcbio/anaconda/envs/bwakit

  added / updated specs:
    - bwakit
    - python=3

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bwakit-0.7.17.dev1         |                0        43.0 MB  bioconda
    c-ares-1.17.1              |       h7f98852_1         109 KB  conda-forge
    fermi2-r170                |       hed695b0_0          95 KB  bioconda
    htsbox-r315                |       hed695b0_0         128 KB  bioconda
    htslib-1.11                |       hd3b49d5_2         1.8 MB  bioconda
    libcurl-7.75.0             |       hc4aaa36_0         328 KB  conda-forge
    libdeflate-1.7             |       h27cfd23_5          55 KB
    libssh2-1.9.0              |       ha56f1ee_6         226 KB  conda-forge
    ropebwt2-r187              |       hed695b0_4          79 KB  bioconda
    samblaster-0.1.20          |       hc9558a2_0          24 KB  bioconda
    samtools-1.11              |       h6270b1f_0         383 KB  bioconda
    seqtk-r82                  |                1          76 KB  bioconda
    trimadap-r2                |       hed695b0_0          33 KB  bioconda
    ------------------------------------------------------------
                                           Total:        46.3 MB

The following NEW packages will be INSTALLED:

  bwa                bioconda/linux-64::bwa-0.7.17-hed695b0_7
  bwakit             bioconda/noarch::bwakit-0.7.17.dev1-0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.17.1-h7f98852_1
  fermi2             bioconda/linux-64::fermi2-r170-hed695b0_0
  htsbox             bioconda/linux-64::htsbox-r315-hed695b0_0
  htslib             bioconda/linux-64::htslib-1.11-hd3b49d5_2
  k8                 bioconda/linux-64::k8-0.2.5-he513fc3_0
  krb5               conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
  libcurl            conda-forge/linux-64::libcurl-7.75.0-hc4aaa36_0
  libdeflate         pkgs/main/linux-64::libdeflate-1.7-h27cfd23_5
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libgcc             conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2
  libnghttp2         conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_0
  libssh2            conda-forge/linux-64::libssh2-1.9.0-ha56f1ee_6
  make               conda-forge/linux-64::make-4.3-hd18ef5c_1
  perl               conda-forge/linux-64::perl-5.32.0-h36c2ea0_0
  ropebwt2           bioconda/linux-64::ropebwt2-r187-hed695b0_4
  samblaster         bioconda/linux-64::samblaster-0.1.20-hc9558a2_0
  samtools           bioconda/linux-64::samtools-1.11-h6270b1f_0
  seqtk              bioconda/linux-64::seqtk-r82-1
  trimadap           bioconda/linux-64::trimadap-r2-hed695b0_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment dv: deepvariant

# All requested packages already installed.

# Installing into conda environment htslib1.10: mosdepth

# All requested packages already installed.

# Installing into conda environment htslib1.11: scramble

## Package Plan ##

  environment location: /apps1/local/share/bcbio/anaconda/envs/htslib1.11

  added / updated specs:
    - python=3
    - scramble

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-2.17                  |         openblas          11 KB  conda-forge
    blas-devel-3.8.0           |      17_openblas          10 KB  conda-forge
    blast-2.10.1               |  pl526he19e7b1_3        20.6 MB  bioconda
    cairo-1.16.0               |    h7979940_1007         1.5 MB  conda-forge
    curl-7.75.0                |       h979ede3_0         147 KB  conda-forge
    entrez-direct-13.9         |  pl526h375a9b1_1         5.2 MB  bioconda
    gcc_impl_linux-64-9.3.0    |      h70c0ae5_18        43.1 MB  conda-forge
    gcc_linux-64-9.3.0         |      hf25ea35_30          23 KB  conda-forge
    gettext-0.19.8.1           |    h0b5b191_1005         3.6 MB  conda-forge
    gfortran_impl_linux-64-9.3.0|      hc4a2995_18        10.1 MB  conda-forge
    gfortran_linux-64-9.3.0    |      hdc58fab_30          22 KB  conda-forge
    gxx_impl_linux-64-9.3.0    |      hd87eabc_18        10.7 MB  conda-forge
    gxx_linux-64-9.3.0         |      h3fbe746_30          23 KB  conda-forge
    harfbuzz-2.7.4             |       h5cf4720_0         1.9 MB  conda-forge
    icu-68.1                   |       h2531618_0        11.8 MB
    libgcc-devel_linux-64-9.3.0|      h7864c58_18         4.0 MB  conda-forge
    libglib-2.66.7             |       h3e27bee_1         3.0 MB  conda-forge
    liblapacke-3.8.0           |      17_openblas          11 KB  conda-forge
    libopenblas-0.3.10         |pthreads_hb3c22a3_5         7.8 MB  conda-forge
    libstdcxx-devel_linux-64-9.3.0|      hb016644_18        13.9 MB  conda-forge
    libxml2-2.9.10             |       h72842e0_3         1.3 MB  conda-forge
    openblas-0.3.10            |pthreads_h43bd3aa_5         8.3 MB  conda-forge
    pango-1.42.4               |       h80147aa_5         533 KB  conda-forge
    pcre2-10.36                |       h032f7d1_1         1.1 MB  conda-forge
    perl-5.26.2                |    h36c2ea0_1008        15.4 MB  conda-forge
    perl-archive-tar-2.32      |          pl526_0          31 KB  bioconda
    perl-io-zlib-1.10          |          pl526_2           9 KB  bioconda
    pixman-0.40.0              |       h36c2ea0_0         627 KB  conda-forge
    r-base-4.0.3               |       h8ff2632_7        23.7 MB  conda-forge
    r-glue-1.4.2               |    r40hcfec24a_0         141 KB  conda-forge
    r-magrittr-2.0.1           |    r40hcfec24a_1         211 KB  conda-forge
    r-rblast-0.99.1            |            r40_3          40 KB  bioconda
    r-stringi-1.5.3            |    r40hcabe038_1         803 KB  conda-forge
    scramble-1.0.1             |       h516909a_0         1.2 MB  bioconda
    xorg-libsm-1.2.3           |    hd9c2040_1000          26 KB  conda-forge
    xorg-libx11-1.7.0          |       h36c2ea0_0         943 KB  conda-forge
    xorg-libxext-1.3.4         |       h7f98852_1          54 KB  conda-forge
    xorg-libxrender-0.9.10     |    h7f98852_1003          32 KB  conda-forge
    xorg-libxt-1.2.1           |       h7f98852_2         375 KB  conda-forge
    zstd-1.4.9                 |       ha95c52a_0         431 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       192.6 MB

The following NEW packages will be INSTALLED:

  _r-mutex           conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
  binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.35.1-h193b22a_2
  binutils_linux-64  conda-forge/linux-64::binutils_linux-64-2.35-h67ddf6f_30
  bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.36.0-r40_0
  bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.24.0-r40h5f743cb_0
  bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.58.0-r40h037d062_0
  bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.26.0-r40_0
  bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.4-r40_0
  bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.42.0-r40h037d062_0
  bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.24.0-r40h037d062_0
  bioconductor-rhts~ bioconda/linux-64::bioconductor-rhtslib-1.22.0-r40h037d062_0
  bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-2.6.0-r40h5f743cb_0
  bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.28.0-r40h037d062_0
  bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.30.0-r40h037d062_0
  bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.36.0-r40h037d062_0
  blast              bioconda/linux-64::blast-2.10.1-pl526he19e7b1_3
  bwidget            conda-forge/linux-64::bwidget-1.9.14-0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.17.1-h7f98852_1
  cairo              conda-forge/linux-64::cairo-1.16.0-h7979940_1007
  curl               conda-forge/linux-64::curl-7.75.0-h979ede3_0
  entrez-direct      bioconda/linux-64::entrez-direct-13.9-pl526h375a9b1_1
  expat              pkgs/main/linux-64::expat-2.2.10-he6710b0_2
  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-hba837de_1004
  freetype           conda-forge/linux-64::freetype-2.10.4-h0708190_1
  fribidi            conda-forge/linux-64::fribidi-1.0.10-h516909a_0
  gcc_impl_linux-64  conda-forge/linux-64::gcc_impl_linux-64-9.3.0-h70c0ae5_18
  gcc_linux-64       conda-forge/linux-64::gcc_linux-64-9.3.0-hf25ea35_30
  gettext            conda-forge/linux-64::gettext-0.19.8.1-h0b5b191_1005
  gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.3.0-hc4a2995_18
  gfortran_linux-64  conda-forge/linux-64::gfortran_linux-64-9.3.0-hdc58fab_30
  graphite2          pkgs/main/linux-64::graphite2-1.3.14-h23475e2_0
  gsl                conda-forge/linux-64::gsl-2.6-he838d99_2
  gxx_impl_linux-64  conda-forge/linux-64::gxx_impl_linux-64-9.3.0-hd87eabc_18
  gxx_linux-64       conda-forge/linux-64::gxx_linux-64-9.3.0-h3fbe746_30
  harfbuzz           conda-forge/linux-64::harfbuzz-2.7.4-h5cf4720_0
  htslib             bioconda/linux-64::htslib-1.11-hd3b49d5_2
  icu                pkgs/main/linux-64::icu-68.1-h2531618_0
  jpeg               conda-forge/linux-64::jpeg-9d-h516909a_0
  kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-h77966d4_13
  krb5               conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
  libcurl            conda-forge/linux-64::libcurl-7.75.0-hc4aaa36_0
  libdeflate         pkgs/main/linux-64::libdeflate-1.7-h27cfd23_5
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libgcc-devel_linu~ conda-forge/linux-64::libgcc-devel_linux-64-9.3.0-h7864c58_18
  libgfortran4       conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_18
  libglib            conda-forge/linux-64::libglib-2.66.7-h3e27bee_1
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
  libnghttp2         conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_0
  libpng             conda-forge/linux-64::libpng-1.6.37-hed695b0_2
  libssh2            conda-forge/linux-64::libssh2-1.9.0-ha56f1ee_6
  libstdcxx-devel_l~ conda-forge/linux-64::libstdcxx-devel_linux-64-9.3.0-hb016644_18
  libtiff            conda-forge/linux-64::libtiff-4.2.0-hdc55705_0
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
  libwebp-base       pkgs/main/linux-64::libwebp-base-1.2.0-h27cfd23_0
  libxcb             pkgs/main/linux-64::libxcb-1.14-h7b6447c_0
  libxml2            conda-forge/linux-64::libxml2-2.9.10-h72842e0_3
  lz4-c              pkgs/main/linux-64::lz4-c-1.9.3-h2531618_0
  make               conda-forge/linux-64::make-4.3-hd18ef5c_1
  pango              conda-forge/linux-64::pango-1.42.4-h80147aa_5
  pcre               pkgs/main/linux-64::pcre-8.44-he6710b0_0
  pcre2              conda-forge/linux-64::pcre2-10.36-h032f7d1_1
  perl               conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
  perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1
  perl-archive-tar   bioconda/linux-64::perl-archive-tar-2.32-pl526_0
  perl-base          bioconda/linux-64::perl-base-2.23-pl526_1
  perl-business-isbn bioconda/linux-64::perl-business-isbn-3.004-pl526_0
  perl-business-isb~ bioconda/linux-64::perl-business-isbn-data-20140910.003-pl526_0
  perl-carp          bioconda/linux-64::perl-carp-1.38-pl526_3
  perl-common-sense  bioconda/linux-64::perl-common-sense-3.74-pl526_2
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-bzip2-2.087-pl526he1b5a44_0
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-zlib-2.087-pl526hc9558a2_0
  perl-constant      bioconda/linux-64::perl-constant-1.33-pl526_1
  perl-data-dumper   bioconda/linux-64::perl-data-dumper-2.173-pl526_0
  perl-digest-hmac   bioconda/linux-64::perl-digest-hmac-1.03-pl526_3
  perl-digest-md5    bioconda/linux-64::perl-digest-md5-2.55-pl526_0
  perl-encode        bioconda/linux-64::perl-encode-2.88-pl526_1
  perl-encode-locale bioconda/linux-64::perl-encode-locale-1.05-pl526_6
  perl-exporter      bioconda/linux-64::perl-exporter-5.72-pl526_1
  perl-exporter-tiny bioconda/linux-64::perl-exporter-tiny-1.002001-pl526_0
  perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1
  perl-file-listing  bioconda/linux-64::perl-file-listing-6.04-pl526_1
  perl-file-path     bioconda/linux-64::perl-file-path-2.16-pl526_0
  perl-file-temp     bioconda/linux-64::perl-file-temp-0.2304-pl526_2
  perl-html-parser   bioconda/linux-64::perl-html-parser-3.72-pl526h6bb024c_5
  perl-html-tagset   bioconda/linux-64::perl-html-tagset-3.20-pl526_3
  perl-html-tree     bioconda/linux-64::perl-html-tree-5.07-pl526_1
  perl-http-cookies  bioconda/linux-64::perl-http-cookies-6.04-pl526_0
  perl-http-daemon   bioconda/linux-64::perl-http-daemon-6.01-pl526_1
  perl-http-date     bioconda/linux-64::perl-http-date-6.02-pl526_3
  perl-http-message  bioconda/linux-64::perl-http-message-6.18-pl526_0
  perl-http-negotia~ bioconda/linux-64::perl-http-negotiate-6.01-pl526_3
  perl-io-compress   bioconda/linux-64::perl-io-compress-2.087-pl526he1b5a44_0
  perl-io-html       bioconda/linux-64::perl-io-html-1.001-pl526_2
  perl-io-socket-ssl bioconda/linux-64::perl-io-socket-ssl-2.066-pl526_0
  perl-io-zlib       bioconda/linux-64::perl-io-zlib-1.10-pl526_2
  perl-json          bioconda/linux-64::perl-json-4.02-pl526_0
  perl-json-xs       bioconda/linux-64::perl-json-xs-2.34-pl526h6bb024c_3
  perl-libwww-perl   bioconda/noarch::perl-libwww-perl-6.39-pl526_0
  perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-0.428-pl526_1
  perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.428-pl526_0
  perl-lwp-mediatyp~ bioconda/linux-64::perl-lwp-mediatypes-6.04-pl526_0
  perl-lwp-protocol~ bioconda/linux-64::perl-lwp-protocol-https-6.07-pl526_4
  perl-mime-base64   bioconda/linux-64::perl-mime-base64-3.15-pl526_1
  perl-mozilla-ca    bioconda/linux-64::perl-mozilla-ca-20180117-pl526_1
  perl-net-http      bioconda/noarch::perl-net-http-6.19-pl526_0
  perl-net-ssleay    bioconda/linux-64::perl-net-ssleay-1.88-pl526h90d6eec_0
  perl-ntlm          bioconda/linux-64::perl-ntlm-1.09-pl526_4
  perl-parent        bioconda/linux-64::perl-parent-0.236-pl526_1
  perl-pathtools     bioconda/linux-64::perl-pathtools-3.75-pl526h14c3975_1
  perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.52-pl526h516909a_0
  perl-socket        bioconda/linux-64::perl-socket-2.027-pl526_1
  perl-storable      bioconda/linux-64::perl-storable-3.15-pl526h14c3975_0
  perl-test-require~ bioconda/linux-64::perl-test-requiresinternet-0.05-pl526_0
  perl-time-local    bioconda/linux-64::perl-time-local-1.28-pl526_1
  perl-try-tiny      bioconda/linux-64::perl-try-tiny-0.30-pl526_1
  perl-types-serial~ bioconda/linux-64::perl-types-serialiser-1.0-pl526_2
  perl-uri           bioconda/linux-64::perl-uri-1.76-pl526_0
  perl-www-robotrul~ bioconda/linux-64::perl-www-robotrules-6.02-pl526_3
  perl-xml-namespac~ bioconda/linux-64::perl-xml-namespacesupport-1.12-pl526_0
  perl-xml-parser    conda-forge/linux-64::perl-xml-parser-2.44_01-pl526ha1d75be_1002
  perl-xml-sax       bioconda/noarch::perl-xml-sax-1.02-pl526_0
  perl-xml-sax-base  bioconda/linux-64::perl-xml-sax-base-1.09-pl526_0
  perl-xml-sax-expat bioconda/linux-64::perl-xml-sax-expat-0.51-pl526_3
  perl-xml-simple    bioconda/linux-64::perl-xml-simple-2.25-pl526_1
  perl-xsloader      bioconda/linux-64::perl-xsloader-0.24-pl526_0
  pixman             conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0
  r-base             conda-forge/linux-64::r-base-4.0.3-h8ff2632_7
  r-bh               conda-forge/noarch::r-bh-1.75.0_0-r40hc72bb7e_0
  r-bitops           conda-forge/linux-64::r-bitops-1.0_6-r40hcdcec82_1004
  r-crayon           conda-forge/noarch::r-crayon-1.4.1-r40hc72bb7e_0
  r-formatr          conda-forge/noarch::r-formatr-1.7-r40h6115d3f_2
  r-futile.logger    conda-forge/noarch::r-futile.logger-1.4.3-r40h6115d3f_1003
  r-futile.options   conda-forge/noarch::r-futile.options-1.0.1-r40h6115d3f_1002
  r-getopt           conda-forge/noarch::r-getopt-1.20.3-r40_2
  r-glue             conda-forge/linux-64::r-glue-1.4.2-r40hcfec24a_0
  r-lambda.r         conda-forge/noarch::r-lambda.r-1.2.4-r40h6115d3f_1
  r-magrittr         conda-forge/linux-64::r-magrittr-2.0.1-r40hcfec24a_1
  r-optparse         conda-forge/noarch::r-optparse-1.6.6-r40h6115d3f_1
  r-rblast           bioconda/linux-64::r-rblast-0.99.1-r40_3
  r-rcurl            conda-forge/linux-64::r-rcurl-1.98_1.2-r40hcdcec82_1
  r-snow             conda-forge/noarch::r-snow-0.4_3-r40h6115d3f_1002
  r-stringi          conda-forge/linux-64::r-stringi-1.5.3-r40hcabe038_1
  r-stringr          conda-forge/noarch::r-stringr-1.4.0-r40h6115d3f_2
  scramble           bioconda/linux-64::scramble-1.0.1-h516909a_0
  sed                conda-forge/linux-64::sed-4.8-he412f7d_0
  sysroot_linux-64   conda-forge/noarch::sysroot_linux-64-2.12-h77966d4_13
  tktable            conda-forge/linux-64::tktable-2.10-hb7b940f_3
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.7.0-h36c2ea0_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.2.1-h7f98852_2
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto        pkgs/main/linux-64::xorg-xproto-7.0.31-h27cfd23_1007
  zstd               conda-forge/linux-64::zstd-1.4.9-ha95c52a_0

The following packages will be DOWNGRADED:

  blas                                       2.108-openblas --> 2.17-openblas
  blas-devel                               3.9.0-8_openblas --> 3.8.0-17_openblas
  libblas                                  3.9.0-8_openblas --> 3.8.0-17_openblas
  libcblas                                 3.9.0-8_openblas --> 3.8.0-17_openblas
  libgfortran-ng                          9.3.0-hff62375_18 --> 7.5.0-h14aa051_18
  liblapack                                3.9.0-8_openblas --> 3.8.0-17_openblas
  liblapacke                               3.9.0-8_openblas --> 3.8.0-17_openblas
  libopenblas                    0.3.12-pthreads_h4812303_1 --> 0.3.10-pthreads_hb3c22a3_5
  openblas                       0.3.12-pthreads_h04b7a96_1 --> 0.3.10-pthreads_h43bd3aa_5

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment python2: bismark, cpat, cutadapt=1.16, dkfz-bias-filter, gemini, gvcf-regions, hap.py, htseq=0.9.1, lumpy-sv, manta, metasv, mirge, phylowgs, platypus-variant, sentieon, smcounter2, smoove, strelka, svtools, svtyper, theta2, tophat, vawk, vcf2db

# All requested packages already installed.

# Installing into conda environment python3: atropos, crossmap

# All requested packages already installed.

# Installing into conda environment r36: ataqv, bioconductor-degreport, bioconductor-deseq2, bioconductor-genomeinfodb, bioconductor-genomeinfodbdata, bioconductor-org.hs.eg.db, bioconductor-purecn>=1.18.0, bioconductor-rtracklayer, bioconductor-txdb.hsapiens.ucsc.hg19.knowngene, bioconductor-txdb.hsapiens.ucsc.hg38.knowngene, bioconductor-tximport, r-janitor, r-optparse, r-pscbs, r-tidyverse

## Package Plan ##

  environment location: /apps1/local/share/bcbio/anaconda/envs/r36

  added / updated specs:
    - ataqv
    - bioconductor-degreport
    - bioconductor-deseq2
    - bioconductor-genomeinfodb
    - bioconductor-genomeinfodbdata
    - bioconductor-org.hs.eg.db
    - bioconductor-purecn[version='>=1.18.0']
    - bioconductor-rtracklayer
    - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
    - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
    - bioconductor-tximport
    - python=3
    - r-janitor
    - r-optparse
    - r-pscbs
    - r-tidyverse

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bioconductor-all-1.32.0    |            r40_0           7 KB  bioconda
    bioconductor-annotate-1.68.0|            r40_0         2.1 MB  bioconda
    bioconductor-complexheatmap-2.6.2|            r40_0         3.0 MB  bioconda
    bioconductor-consensusclusterplus-1.54.0|            r40_0         342 KB  bioconda
    bioconductor-degreport-1.26.0|            r40_0         3.0 MB  bioconda
    bioconductor-deseq2-1.30.0 |    r40h5f743cb_0         2.7 MB  bioconda
    bioconductor-edger-3.32.0  |    r40h5f743cb_0         2.4 MB  bioconda
    bioconductor-genefilter-1.72.0|    r40hc6cf775_0         1.8 MB  bioconda
    bioconductor-geneplotter-1.68.0|            r40_0         1.5 MB  bioconda
    bioconductor-limma-3.46.0  |    r40h037d062_0         2.8 MB  bioconda
    bioconductor-tximport-1.18.0|            r40_0         364 KB  bioconda
    pandoc-2.12                |       h7f98852_0        12.4 MB  conda-forge
    r-base64enc-0.1_3          | r40hcdcec82_1004          43 KB  conda-forge
    r-broom-0.7.5              |    r40hc72bb7e_0         1.7 MB  conda-forge
    r-cairo-1.5_12.2           |    r40hcdcec82_0          94 KB  conda-forge
    r-cellranger-1.1.0         | r40h6115d3f_1003         108 KB  conda-forge
    r-circlize-0.4.12          |    r40hc72bb7e_0         3.2 MB  conda-forge
    r-clipr-0.7.1              |    r40h142f84f_0          65 KB  conda-forge
    r-clue-0.3_57              |    r40h516909a_2         1.0 MB  conda-forge
    r-cluster-2.1.0            |    r40h31ca83e_4         553 KB  conda-forge
    r-cowplot-1.1.1            |    r40hc72bb7e_0         1.3 MB  conda-forge
    r-cpp11-0.2.6              |    r40hc72bb7e_0         154 KB  conda-forge
    r-forcats-0.5.1            |    r40hc72bb7e_0         377 KB  conda-forge
    r-fs-1.5.0                 |    r40h0357c0b_0         515 KB  conda-forge
    r-getoptlong-1.0.5         |    r40hc72bb7e_0         1.0 MB  conda-forge
    r-ggdendro-0.1.22          |    r40h6115d3f_0         195 KB  conda-forge
    r-ggrepel-0.8.2            |    r40h0357c0b_1         653 KB  conda-forge
    r-globaloptions-0.1.2      |            r40_0         472 KB  conda-forge
    r-haven-2.3.1              |    r40hde08347_0         373 KB  conda-forge
    r-highr-0.8                |    r40h6115d3f_2          58 KB  conda-forge
    r-htmltools-0.5.0          |    r40h0357c0b_0         233 KB  conda-forge
    r-janitor-2.1.0            |    r40hc72bb7e_0         243 KB  conda-forge
    r-knitr-1.31               |    r40hc72bb7e_0         1.3 MB  conda-forge
    r-lasso2-1.2_21.1          |    r40h0eb13af_0         280 KB  conda-forge
    r-locfit-1.5_9.4           |    r40hcdcec82_1         560 KB  conda-forge
    r-logging-0.10_108         |            r40_2         177 KB  conda-forge
    r-lubridate-1.7.9.2        |    r40he524a50_0         1.1 MB  conda-forge
    r-markdown-1.1             |    r40hcdcec82_1         143 KB  conda-forge
    r-mnormt-1.5_7             |    r40h31ca83e_2         113 KB  conda-forge
    r-modelr-0.1.8             |    r40h6115d3f_0         218 KB  conda-forge
    r-nozzle.r1-1.1_1          |         r40_1003         374 KB  conda-forge
    r-png-0.1_7                | r40hcdcec82_1004          58 KB  conda-forge
    r-psych-2.0.12             |    r40hc72bb7e_0         4.6 MB  conda-forge
    r-rcpparmadillo-0.10.1.2.0 |    r40hfbb317b_0         1.2 MB  conda-forge
    r-readr-1.4.0              |    r40h1b71b39_0         861 KB  conda-forge
    r-readxl-1.3.1             |    r40hde08347_4         859 KB  conda-forge
    r-rematch-1.0.1            | r40h6115d3f_1003          19 KB  conda-forge
    r-reprex-1.0.0             |    r40hc72bb7e_0         483 KB  conda-forge
    r-reshape-0.8.8            |    r40hcdcec82_2         175 KB  conda-forge
    r-reshape2-1.4.4           |    r40h0357c0b_1         135 KB  conda-forge
    r-rjson-0.2.20             | r40h0357c0b_1002         146 KB  conda-forge
    r-rmarkdown-2.7            |    r40hc72bb7e_0         3.1 MB  conda-forge
    r-rvest-0.3.6              |    r40h6115d3f_0         1.5 MB  conda-forge
    r-selectr-0.4_2            |    r40h6115d3f_1         449 KB  conda-forge
    r-shape-1.4.5              |            r40_0         795 KB  conda-forge
    r-snakecase-0.11.0         |    r40h6115d3f_2         176 KB  conda-forge
    r-survival-3.2_7           |    r40hcdcec82_0         7.6 MB  conda-forge
    r-tidyr-1.1.2              |    r40h0357c0b_0         806 KB  conda-forge
    r-tidyverse-1.3.0          |    r40h6115d3f_2         452 KB  conda-forge
    r-tinytex-0.30             |    r40hc72bb7e_0         123 KB  conda-forge
    r-xfun-0.19                |    r40h9e2df91_0         293 KB  conda-forge
    r-xtable-1.8_4             |    r40h6115d3f_3         697 KB  conda-forge
    r-yaml-2.2.1               |    r40hcdcec82_1         117 KB  conda-forge
    xorg-libxt-1.2.0           |       h516909a_0         374 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        73.5 MB

The following NEW packages will be INSTALLED:

  bioconductor-all   bioconda/noarch::bioconductor-all-1.32.0-r40_0
  bioconductor-anno~ bioconda/noarch::bioconductor-annotate-1.68.0-r40_0
  bioconductor-comp~ bioconda/noarch::bioconductor-complexheatmap-2.6.2-r40_0
  bioconductor-cons~ bioconda/noarch::bioconductor-consensusclusterplus-1.54.0-r40_0
  bioconductor-degr~ bioconda/noarch::bioconductor-degreport-1.26.0-r40_0
  bioconductor-dese~ bioconda/linux-64::bioconductor-deseq2-1.30.0-r40h5f743cb_0
  bioconductor-edger bioconda/linux-64::bioconductor-edger-3.32.0-r40h5f743cb_0
  bioconductor-gene~ bioconda/linux-64::bioconductor-genefilter-1.72.0-r40hc6cf775_0
  bioconductor-gene~ bioconda/noarch::bioconductor-geneplotter-1.68.0-r40_0
  bioconductor-limma bioconda/linux-64::bioconductor-limma-3.46.0-r40h037d062_0
  bioconductor-txim~ bioconda/noarch::bioconductor-tximport-1.18.0-r40_0
  pandoc             conda-forge/linux-64::pandoc-2.12-h7f98852_0
  r-base64enc        conda-forge/linux-64::r-base64enc-0.1_3-r40hcdcec82_1004
  r-broom            conda-forge/noarch::r-broom-0.7.5-r40hc72bb7e_0
  r-cairo            conda-forge/linux-64::r-cairo-1.5_12.2-r40hcdcec82_0
  r-cellranger       conda-forge/noarch::r-cellranger-1.1.0-r40h6115d3f_1003
  r-circlize         conda-forge/noarch::r-circlize-0.4.12-r40hc72bb7e_0
  r-clipr            conda-forge/noarch::r-clipr-0.7.1-r40h142f84f_0
  r-clue             conda-forge/linux-64::r-clue-0.3_57-r40h516909a_2
  r-cluster          conda-forge/linux-64::r-cluster-2.1.0-r40h31ca83e_4
  r-cowplot          conda-forge/noarch::r-cowplot-1.1.1-r40hc72bb7e_0
  r-cpp11            conda-forge/noarch::r-cpp11-0.2.6-r40hc72bb7e_0
  r-forcats          conda-forge/noarch::r-forcats-0.5.1-r40hc72bb7e_0
  r-fs               conda-forge/linux-64::r-fs-1.5.0-r40h0357c0b_0
  r-getoptlong       conda-forge/noarch::r-getoptlong-1.0.5-r40hc72bb7e_0
  r-ggdendro         conda-forge/noarch::r-ggdendro-0.1.22-r40h6115d3f_0
  r-ggrepel          conda-forge/linux-64::r-ggrepel-0.8.2-r40h0357c0b_1
  r-globaloptions    conda-forge/noarch::r-globaloptions-0.1.2-r40_0
  r-haven            conda-forge/linux-64::r-haven-2.3.1-r40hde08347_0
  r-highr            conda-forge/noarch::r-highr-0.8-r40h6115d3f_2
  r-htmltools        conda-forge/linux-64::r-htmltools-0.5.0-r40h0357c0b_0
  r-janitor          conda-forge/noarch::r-janitor-2.1.0-r40hc72bb7e_0
  r-knitr            conda-forge/noarch::r-knitr-1.31-r40hc72bb7e_0
  r-lasso2           conda-forge/linux-64::r-lasso2-1.2_21.1-r40h0eb13af_0
  r-locfit           conda-forge/linux-64::r-locfit-1.5_9.4-r40hcdcec82_1
  r-logging          conda-forge/noarch::r-logging-0.10_108-r40_2
  r-lubridate        conda-forge/linux-64::r-lubridate-1.7.9.2-r40he524a50_0
  r-markdown         conda-forge/linux-64::r-markdown-1.1-r40hcdcec82_1
  r-mnormt           conda-forge/linux-64::r-mnormt-1.5_7-r40h31ca83e_2
  r-modelr           conda-forge/noarch::r-modelr-0.1.8-r40h6115d3f_0
  r-nozzle.r1        conda-forge/noarch::r-nozzle.r1-1.1_1-r40_1003
  r-plyr             conda-forge/linux-64::r-plyr-1.8.6-r40h0357c0b_1
  r-png              conda-forge/linux-64::r-png-0.1_7-r40hcdcec82_1004
  r-psych            conda-forge/noarch::r-psych-2.0.12-r40hc72bb7e_0
  r-rcpparmadillo    conda-forge/linux-64::r-rcpparmadillo-0.10.1.2.0-r40hfbb317b_0
  r-readr            conda-forge/linux-64::r-readr-1.4.0-r40h1b71b39_0
  r-readxl           conda-forge/linux-64::r-readxl-1.3.1-r40hde08347_4
  r-rematch          conda-forge/noarch::r-rematch-1.0.1-r40h6115d3f_1003
  r-reprex           conda-forge/noarch::r-reprex-1.0.0-r40hc72bb7e_0
  r-reshape          conda-forge/linux-64::r-reshape-0.8.8-r40hcdcec82_2
  r-reshape2         conda-forge/linux-64::r-reshape2-1.4.4-r40h0357c0b_1
  r-rjson            conda-forge/linux-64::r-rjson-0.2.20-r40h0357c0b_1002
  r-rmarkdown        conda-forge/noarch::r-rmarkdown-2.7-r40hc72bb7e_0
  r-rvest            conda-forge/noarch::r-rvest-0.3.6-r40h6115d3f_0
  r-selectr          conda-forge/noarch::r-selectr-0.4_2-r40h6115d3f_1
  r-shape            conda-forge/noarch::r-shape-1.4.5-r40_0
  r-snakecase        conda-forge/noarch::r-snakecase-0.11.0-r40h6115d3f_2
  r-survival         conda-forge/linux-64::r-survival-3.2_7-r40hcdcec82_0
  r-tidyr            conda-forge/linux-64::r-tidyr-1.1.2-r40h0357c0b_0
  r-tidyverse        conda-forge/noarch::r-tidyverse-1.3.0-r40h6115d3f_2
  r-tinytex          conda-forge/noarch::r-tinytex-0.30-r40hc72bb7e_0
  r-xfun             conda-forge/linux-64::r-xfun-0.19-r40h9e2df91_0
  r-xtable           conda-forge/noarch::r-xtable-1.8_4-r40h6115d3f_3
  r-yaml             conda-forge/linux-64::r-yaml-2.2.1-r40hcdcec82_1
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.2.0-h516909a_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
# Installing into conda environment samtools0: ericscript

# All requested packages already installed.

Creating manifest of installed packages in /apps1/local/share/bcbio/manifest
Third party tools upgrade complete.
Upgrade completed successfully.

But still the bcbio run failed because dplyr version is too low. Can you check this for me too? Thank you.

Running bcbio version: 1.2.7
global config: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbio_system.yaml
run info config: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/config/K0008-K0011_RNA_updated.yaml
[2021-03-09T21:53Z] System YAML configuration: /apps1/local/share/bcbio/galaxy/bcbio_system.yaml.
[2021-03-09T21:53Z] Locale set to C.UTF-8.
[2021-03-09T21:53Z] Resource requests: picard; memory: 3.00; cores: 16
[2021-03-09T21:53Z] Configuring 8 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[2021-03-09T21:53Z] Timing: organize samples
[2021-03-09T21:53Z] multiprocessing: organize_samples
[2021-03-09T21:53Z] Using input YAML configuration: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/config/K0008-K0011_RNA_updated.yaml
[2021-03-09T21:53Z] Checking sample YAML configuration: /apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/config/K0008-K0011_RNA_updated.yaml
[2021-03-09T21:53Z] Retreiving program versions from /apps1/local/share/bcbio/manifest/python-packages.yaml.
[2021-03-09T21:53Z] Retreiving program versions from /apps1/local/share/bcbio/manifest/r-packages.yaml.
[2021-03-09T21:53Z] Testing minimum versions of installed programs
[2021-03-09T21:53Z] multiprocessing: prepare_sample
[2021-03-09T21:53Z] Preparing K0006-BF1-RNAseq
[2021-03-09T21:53Z] Preparing K0011-BF1-RNAseq
[2021-03-09T21:53Z] Preparing K0011-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0009-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0008-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0006-AF1-RNAseq
[2021-03-09T21:53Z] Preparing K0008-AF1-LMDRNAseq
[2021-03-09T21:53Z] Preparing K0010-AF1-RNAseq
[2021-03-09T21:53Z] Resource requests: picard, samtools, star; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16
[2021-03-09T21:53Z] Configuring 6 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2021-03-09T21:53Z] Timing: alignment
[2021-03-09T21:53Z] multiprocessing: disambiguate_split
[2021-03-09T21:53Z] multiprocessing: process_alignment
[2021-03-09T21:53Z] Resource requests: cufflinks, samtools; memory: 3.00, 3.00; cores: 16, 16
[2021-03-09T21:53Z] Configuring 6 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2021-03-09T21:53Z] Timing: disambiguation
[2021-03-09T21:53Z] Timing: transcript assembly
[2021-03-09T21:53Z] Timing: estimate expression (threaded)
[2021-03-09T21:53Z] multiprocessing: generate_transcript_counts
[2021-03-09T21:53Z] multiprocessing: run_kallisto_index
[2021-03-09T21:53Z] multiprocessing: run_kallisto_rnaseq
[2021-03-09T21:53Z] multiprocessing: run_salmon_index
[2021-03-09T21:53Z] multiprocessing: run_salmon_reads
[2021-03-09T21:53Z] multiprocessing: detect_fusions
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  with h5py.File(h5) as f:
/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/rnaseq/pizzly.py:31: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
  with h5py.File(h5) as f:
[2021-03-09T21:53Z] Resource requests: dexseq, express; memory: 10.00, 8.00; cores: 1, 1
[2021-03-09T21:53Z] Configuring 8 jobs to run, using 1 cores each with 10.00g of memory reserved for each job
[2021-03-09T21:53Z] Timing: estimate expression (single threaded)
[2021-03-09T21:53Z] Loading tximport.
[2021-03-09T21:53Z] Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
[2021-03-09T21:53Z]  namespace ‘dplyr’ 1.0.2 is already loaded, but >= 1.0.3 is required
[2021-03-09T21:53Z] Execution halted
[2021-03-09T21:53Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/apps1/local/share/bcbio/anaconda/envs/r36/bin/Rscript --vanilla -e library(tidyverse);salmon_files = list.files("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/salmon", pattern="quant.sf", recursive=TRUE, full.names=TRUE);tx2gene = readr::read_csv("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/inputs/transcriptome/tx2gene.csv", col_names=c("transcript", "gene")); samples = basename(dirname(salmon_files));names(salmon_files) = samples;txi = tximport::tximport(salmon_files, type="salmon", tx2gene=tx2gene, countsFromAbundance="lengthScaledTPM", dropInfReps=TRUE);readr::write_csv(round(txi$counts) %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmpd1qg0wnz/tximport-counts.csv");readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmps3yflioo/tximport-tpm.csv");
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘dplyr’ 1.0.2 is already loaded, but >= 1.0.3 is required
Execution halted
' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/apps1/local/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/apps1/local/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 264, in rnaseqpipeline
    samples = rnaseq.combine_files(samples)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/rnaseq.py", line 489, in combine_files
    tximport = load_tximport(data)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/rnaseq.py", line 556, in load_tximport
    do.run([rcmd, "--vanilla", "-e", render_string], f"Loading tximport.")
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/apps1/local/share/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/apps1/local/share/bcbio/anaconda/envs/r36/bin/Rscript --vanilla -e library(tidyverse);salmon_files = list.files("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/salmon", pattern="quant.sf", recursive=TRUE, full.names=TRUE);tx2gene = readr::read_csv("/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/inputs/transcriptome/tx2gene.csv", col_names=c("transcript", "gene")); samples = basename(dirname(salmon_files));names(salmon_files) = samples;txi = tximport::tximport(salmon_files, type="salmon", tx2gene=tx2gene, countsFromAbundance="lengthScaledTPM", dropInfReps=TRUE);readr::write_csv(round(txi$counts) %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmpd1qg0wnz/tximport-counts.csv");readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "/apps2/data/K008-K0011_Target_Discovery/K0008-K0011_RNA_updated/work/bcbiotx/tmps3yflioo/tximport-tpm.csv");
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘dplyr’ 1.0.2 is already loaded, but >= 1.0.3 is required
Execution halted
' returned non-zero exit status 1.
tykim0109 commented 3 years ago

@naumenko-sa After upgrading tools. Below is the R packages installed in r36 environment. I don't find anything wrong. tidyverse and dplyr look all ok. I'd appreciate if you tell me what else I need to do. Thank you so much.

ubuntu@ip-172-***$ conda activate r36
ubuntu@ip-172-***$ R

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(tidyverse)
Error: package or namespace load failed for ‘tidyverse’:
 .onAttach failed in attachNamespace() for 'tidyverse', details:
  call: clienv$num_colors[[std]]
  error: subscript out of bounds
> print(paste("R", getRversion()))
[1] "R 3.5.1"
> print("-------------")
[1] "-------------"
> for (package_name in sort(loadedNamespaces())) {
+     print(paste(package_name, packageVersion(package_name)))
+ }
[1] "assertthat 0.2.1"
[1] "backports 1.1.6"
[1] "base 3.5.1"
[1] "broom 0.5.6"
[1] "cellranger 1.1.0"
[1] "colorspace 1.4.1"
[1] "compiler 3.5.1"
[1] "crayon 1.4.0"
[1] "datasets 3.5.1"
[1] "DBI 1.1.1"
[1] "dbplyr 1.4.3"
[1] "dplyr 1.0.5"
[1] "ellipsis 0.3.1"
[1] "forcats 0.5.1"
[1] "fs 1.4.1"
[1] "generics 0.1.0"
[1] "ggplot2 3.3.3"
[1] "glue 1.4.0"
[1] "graphics 3.5.1"
[1] "grDevices 3.5.1"
[1] "grid 3.5.1"
[1] "gtable 0.3.0"
[1] "haven 2.2.0"
[1] "hms 1.0.0"
[1] "httr 1.4.2"
[1] "jsonlite 1.7.2"
[1] "lattice 0.20.41"
[1] "lifecycle 1.0.0"
[1] "lubridate 1.7.8"
[1] "magrittr 1.5"
[1] "methods 3.5.1"
[1] "modelr 0.1.8"
[1] "munsell 0.5.0"
[1] "nlme 3.1.147"
[1] "pillar 1.4.7"
[1] "pkgconfig 2.0.3"
[1] "purrr 0.3.4"
[1] "R6 2.5.0"
[1] "Rcpp 1.0.4.6"
[1] "readr 1.3.1"
[1] "readxl 1.3.1"
[1] "reprex 1.0.0"
[1] "rlang 0.4.10"
[1] "rstudioapi 0.13"
[1] "rvest 0.3.6"
[1] "scales 1.1.1"
[1] "stats 3.5.1"
[1] "stringi 1.5.3"
[1] "stringr 1.4.0"
[1] "tibble 3.0.1"
[1] "tidyr 1.0.2"
[1] "tidyselect 1.1.0"
[1] "tidyverse 1.3.0"
[1] "tools 3.5.1"
[1] "utils 3.5.1"
[1] "vctrs 0.3.6"
[1] "xml2 1.3.2"
naumenko-sa commented 3 years ago

There is some installation issue in r36 environment, the purpose of having that environment is to have R>3.5.1 for PureCN and bcbio2se,

For example, in the bcbio installation available to me:

$ conda activate r36
(r36) $ which R
/n/app/bcbio/dev/anaconda/envs/r36/bin/R
(r36) $ R

R version **4.0.3** (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

Also:

$ conda list -n r36 r-base
r-base                    4.0.3                hfb3ec26_0    conda-forge
r-base64enc               0.1_3           r40hcdcec82_1004    conda-forge
$ conda list -n r36 r-tidyverse
r-tidyverse               1.3.0             r40h6115d3f_2    conda-forge
$ conda list -n r36 python
python                    3.7.8           h6f2ec95_0_cpython    conda-forge
python_abi                3.7                     1_cp37m    conda-forge

I think you may either try re-installing bcbio (you could keep and reuse genomes), or to 1) delete r36 environment with conda; 2) create r36 conda environment with python=3.7.8 and r packages listed here for r36: https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml

Sergey

tykim0109 commented 3 years ago

Thank you Sergey @naumenko-sa I re-installed bcbio (reuse genomes) and now it's working fine. Thank you for your help.