nf-core / clipseq Goto Github PK

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

Home Page: https://nf-co.re/clipseq

License: MIT License

Dockerfile 0.51% HTML 1.76% Python 11.39% Nextflow 65.19% Perl 2.69% Groovy 18.47%

workflow pipeline nextflow clip nf-core peak-calling clip-seq rna-rbp-interactions

clipseq's Introduction

Introduction

nf-core/clipseq is a bioinformatics best-practice analysis pipeline for CLIP (cross-linking and immunoprecipitation) sequencing data analysis to study RNA-protein interactions.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Pipeline Summary

By default, the pipeline currently performs the following:

Adapter and quality trimming (Cutadapt)
Pre-mapping to e.g. rRNA and tRNA sequences (Bowtie 2)
Genome mapping (STAR)
UMI-based deduplication (UMI-tools)
Crosslink identification (BEDTools)
Bedgraph coverage track generation (BEDTools)
Peak calling (multiple options):
- iCount
- Paraclu
- PureCLIP
- Piranha
Motif detection (DREME)
Quality control:
- Sequencing quality control (FastQC)
- Library complexity (Preseq)
- Regional distribution (RSeQC)
Overall pipeline run and QC summaries and peak calling comparisons (MultiQC)

Quick Start

Install nextflow
Install any of Docker, Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs)
Download the pipeline and test it on a minimal dataset with a single command:
```
nextflow run nf-core/clipseq -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
```
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

Start running your own analysis!

nextflow run nf-core/clipseq -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '[path to design file]' --fasta '[path to genome FASTA]'

See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/clipseq pipeline comes with documentation about the pipeline: usage and output.

Credits

nf-core/clipseq was originally written by Charlotte West (@charlotte-west) and Anob Chakrabarti (@amchakra) from Luscombe Lab at The Francis Crick Institute, London, UK.

It started life in April 2020 as a Nextflow DSL2 Luscombe Lab (@luslab) lockdown hackathon day and we thank all the lab members for their early contributions.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #clipseq channel (you can join with this invite).

Citations

If you use nf-core/clipseq for your analysis, please cite it using the following doi: 10.5281/zenodo.4723016

References of tools and data used in this pipeline can be found in CITATIONS.md

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

clipseq's People

Contributors

Stargazers

Watchers

clipseq's Issues

alternative motifs to peka (homer,streme)

refactor sample sheets to enable group and input analysis

as above ^

2 new samplesheets:

fastq input
bam - group analysis input

arrange a la nf-core/rnasplice

https://github.com/nf-core/rnasplice/blob/dev/subworkflows/local/input_check.nf

2.0 peaks arent called in test full small

Check Documentation

I have checked the following places for your error:

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

Command line:
See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

The command used to run the pipeline
The .nextflow.log file

System

Hardware:
Executor:
OS:
Version

Nextflow Installation

Version:

Container engine

Engine:
version:
Image tag:

Additional context

MODULE: pureclip

allow control input to pureclip

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

iGenomes path is not correct

Hi all,

First of all thank you for developing the pipeline. I am running into what I think is bug but you might tell me better what is going on. I think it is an issue with the path to the AWS genomes.

Check Documentation

I have checked the following places for your error:

Description of the bug

When I ran the test pipeline everyting works fine (log at the bottom), however when I do a proper run the genome is not found:

adomingues@ad-genome:~/genomics/projects/RBM20_clip$ nextflow run nf-core/clipseq --input "results/design.txt" --genome 'GRCh38' -profile "singularity" --smrna_org "human" --peakcaller all -r "dev"
N E X T F L O W  ~  version 20.10.0
Launching `nf-core/clipseq` [gloomy_caravaggio] - revision: a3c52c22d5 [dev]
s3:/ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf (No such file or directory)

 -- Check script '/home/adomingues/.nextflow/assets/nf-core/clipseq/main.nf' at line: 1465 or see '.nextflow.log' file for more details

It seems to me that the issue is that the path is malformed. The error message states s3:/ngi-igenomes/ when, and judging from the nf-core docs, it should have been s3://ngi-igenomes/.

I also checked the log at the line referenced, but there is nothing I can deduce from there at what the error is:

adomingues@ad-genome:~/genomics/projects/RBM20_clip$ sed -n 1464,1470p /home/adomingues/.nextflow/assets/nf-core/clipseq/main.nf

  boolean gencode = false
  f.withReader { r ->
    while( count<n && ( !gene && ( !ensembl || !gencode ) ) ) {
        line = r.readLine();
        count = count + 1;
        if (!gene) {
            if (line =~ /\bgene\b/) {

I have also tried other genome versions, GRCh37 and hg38, but the error persists. Any help would be appreciated.

Cheers.

Log files

Have you provided the following extra information/files:

[ X The command used to run the pipeline
[ X] The .nextflow.log file

System

Hardware: HPC, VM
Executor: local
OS:Ubuntu Linux
Version: 20.04

Nextflow Installation

Version: 20.10.0.5430

Container engine

Engine: Singularity
version: 2.6.1-dist
Image tag: nfcore/clipseq:dev

remove fastq2 from samplesheet, SAMPLESHEET_CHECK and PARSE_FASTQ_INPUT modules, explain in docs why

Pipeline has no release, but not WIP or UNDER CONSTRUCTION warning

Check Documentation

I have checked the following places for your error:

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

Command line:
See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

The command used to run the pipeline
The .nextflow.log file

System

Hardware:
Executor:
OS:
Version

Nextflow Installation

Version:

Container engine

Engine:
version:
Image tag:

Additional context

Add figures to output docs

Is your feature request related to a problem? Please describe

No figures in the output docs to complement descriptions

Describe the solution you'd like

Use figures from MultiQC output from the AWS megatest run in the output docs

Additional context

To do in the next release

support for eclip paired end reads

peak calling subworkflow

Conda env fails to create

Check Documentation

I have checked the following places for your error:

Description of the bug

The conda environment fails to create both with nextflow and by itself.

Steps to reproduce

Steps to reproduce the behavior:
for the documented install process:

`conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda create --name env_nf nextflow`

for just trying the clipseq conda environment

conda env create -f clipseq/environment.yml -n clipseq

Expected behaviour

conda environment creates successfully

Log files

Have you provided the following extra information/files:

The command used to run the pipeline
The .nextflow.log file

System

Hardware:
Executor:
OS:
Version

Nextflow Installation

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Container engine

Engine:
version:
Image tag:

Additional context

after just trying to create the base conda image i get

`Collecting package metadata (repodata.json): done
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Building graph of deps: 0%| Examining conda-forge::pigz=2.3.4: 0%| Examining bioconda::fastqc=0.11.9: 4%|███████▉ Examining @/linux-64::__archspec==x86_64=0: 8%|███████████████▏ Examining bioconda::preseq=2.0.3: 12%|████████████████████████ Examining bioconda::pureclip=1.3.1: 16%|███████████████████████████████▋ Examining bioconda::pureclip=1.3.1: 20%|███████████████████████████████████████▌ Examining conda-forge::python=3.7.3: 20%|███████████████████████████████████████▍ Examining bioconda::samtools=1.11: 24%|███████████████████████████████████████████████▊ Examining bioconda::umi_tools=1.1.1: 28%|███████████████████████████████████████████████████████▏ Examining @/linux-64::__glibc==2.31=0: 32%|██████████████████████████████████████████████████████████████▍ Examining @/linux-64::__glibc==2.31=0: 36%|██████████████████████████████████████████████████████████████████████▏ Examining bioconda::star=2.6.1d: 36%|████████████████████████████████████████████████████████████████████████▎ Examining bioconda::cutadapt=3.0: 40%|███████████████████████████████████████████████████████████████████████████████▌ Examining bioconda::piranha=1.2.1: 44%|███████████████████████████████████████████████████████████████████████████████████████ Examining bioconda::piranha=1.2.1: 48%|███████████████████████████████████████████████████████████████████████████████████████████████ Examining bioconda::bowtie2=2.4.2: 48%|███████████████████████████████████████████████████████████████████████████████████████████████ Examining conda-forge::pygments=2.5.2: 52%|████████████████████████████████████████████████████████████████████████████████████████████████████▉ Examining conda-forge::pygments=2.5.2: 56%|████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ Examining bioconda::subread=2.0.1: 56%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████▉ Examining bioconda::paraclu=9: 60%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ Examining bioconda::paraclu=9: 64%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ Examining bioconda::rseqc=4.0.0: 64%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ Examining @/linux-64::__linux==5.4.0=0: 68%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ Examining @/linux-64::__linux==5.4.0=0: 72%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉ Examining bioconda::bedtools=2.29.2: 72%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ Examining conda-forge::perl=5.26.2: 76%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋Examining bioconda::meme=5.1.1: 80%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining bioconda::meme=5.1.1: 84%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining bioconda::icount=2.0.0: 84%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conda-forge::pymdown-extensions=6.0: 88%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conda-forge::pymdown-extensions=6.0: 92%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining bioconda::multiqc=1.9: 92%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining bioconda::multiqc=1.9: 96%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conda-forge::markdown=3.1.1: 96%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conda-forge::markdown=3.1.1: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ Determining conflicts: 0%| Examining conflict for pigz cutadapt icount: 0%| Examining conflict for pigz fastqc preseq pureclip python samtools umi_tools cutadapt piranha bowtie2 pygments subread paraclu rseqc bedtools meme icount pymdown-extensions multiqc markdown: Examining conflict for pigz fastqc preseq pureclip python samtools umi_tools cutadapt piranha bowtie2 pygments subread paraclu rseqc bedtools meme icount pymdown-extensions multiqc markdown: Examining conflict for cutadapt piranha bowtie2 samtools pigz umi_tools subread bedtools perl paraclu rseqc meme __glibc preseq python: 8%|███████▊ Examining conflict for cutadapt piranha bowtie2 samtools pigz umi_tools subread bedtools perl paraclu rseqc meme __glibc preseq python: 12%|███████████▊ Examining conflict for cutadapt piranha bowtie2 samtools pigz umi_tools subread bedtools perl paraclu rseqc meme preseq python: 12%|████████████▋ Examining conflict for cutadapt piranha bowtie2 samtools pigz umi_tools subread bedtools perl paraclu rseqc meme preseq python: 16%|████████████████▉ Examining conflict for pigz fastqc preseq pureclip python samtools umi_tools cutadapt piranha bowtie2 pygments subread paraclu rseqc bedtools perl meme icount pymdown-extensions multiqc markdExamining conflict for pigz fastqc preseq pureclip python samtools umi_tools cutadapt piranha bowtie2 pygments subread paraclu rseqc bedtools perl meme icount pymdown-extensions multiqc markdExamining conflict for fastqc pureclip meme: 20%|█████████████████████████████████████▊ Examining conflict for fastqc pureclip meme: 24%|█████████████████████████████████████████████▎ Examining conflict for umi_tools icount fastqc rseqc multiqc: 24%|█████████████████████████████████████████▎ Examining conflict for umi_tools icount fastqc rseqc multiqc: 28%|████████████████████████████████████████████████▏ Examining conflict for fastqc bowtie2: 28%|██████████████████████████████████████████████████████▌ Examining conflict for fastqc bowtie2: 32%|██████████████████████████████████████████████████████████████▍ Examining conflict for fastqc rseqc: 32%|███████████████████████████████████████████████████████████████ Examining conflict for fastqc rseqc: 36%|██████████████████████████████████████████████████████████████████████▉ Examining conflict for umi_tools meme icount fastqc rseqc pureclip multiqc: 36%|████████████████████████████████████████████████████████▉ Examining conflict for umi_tools meme icount fastqc rseqc pureclip multiqc: 40%|██████████████████████████████████████████████████████████████▊ Examining conflict for fastqc pureclip rseqc meme: 40%|████████████████████████████████████████████████████████████████████████▊ Examining conflict for fastqc pureclip rseqc meme: 44%|████████████████████████████████████████████████████████████████████████████████ Examining conflict for bowtie2 perl meme fastqc pureclip: 44%|█████████████████████████████████████████████████████████████████████████████ Examining conflict for bowtie2 perl meme fastqc pureclip: 48%|████████████████████████████████████████████████████████████████████████████████████ Examining conflict for cutadapt bowtie2 pygments umi_tools meme icount fastqc rseqc pymdown-extensions multiqc markdown: 48%|█████████████████████████████████████████████████████▊ Examining conflict for cutadapt bowtie2 pygments umi_tools meme icount fastqc rseqc pymdown-extensions multiqc markdown: 52%|██████████████████████████████████████████████████████████▏ Examining conflict for cutadapt piranha bowtie2 samtools umi_tools pygments bedtools meme icount paraclu fastqc rseqc pymdown-extensions multiqc preseq pureclip python markdown: 52%|████████Examining conflict for cutadapt piranha bowtie2 samtools umi_tools pygments bedtools meme icount paraclu fastqc rseqc pymdown-extensions multiqc preseq pureclip python markdown: 56%|████████Examining conflict for fastqc meme: 56%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████▎ Examining conflict for fastqc meme: 60%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ Examining conflict for piranha umi_tools icount rseqc preseq multiqc: 60%|█████████████████████████████████████████████████████████████████████████████████████████████████▊ Examining conflict for piranha umi_tools icount rseqc preseq multiqc: 64%|████████████████████████████████████████████████████████████████████████████████████████████████████████▎ Examining conflict for preseq piranha: 64%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▏ Examining conflict for preseq piranha: 68%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▉ Examining conflict for piranha umi_tools meme icount rseqc preseq multiqc: 68%|███████████████████████████████████████████████████████████████████████████████████████████████████████████▍ Examining conflict for piranha umi_tools meme icount rseqc preseq multiqc: 72%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for piranha umi_tools meme icount rseqc preseq pureclip: 72%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for piranha umi_tools meme icount rseqc preseq pureclip: 76%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for rseqc preseq piranha: 76%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for rseqc preseq piranha: 80%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for piranha umi_tools meme rseqc preseq: 80%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for piranha umi_tools meme rseqc preseq: 84%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for samtools umi_tools icount rseqc pureclip: 84%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for samtools umi_tools icount rseqc pureclip: 88%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for cutadapt piranha bowtie2 pygments umi_tools meme icount rseqc pymdown-extensions multiqc pureclip python markdown: 88%|████████████████████████████████████████████████Examining conflict for cutadapt piranha bowtie2 pygments umi_tools meme icount rseqc pymdown-extensions multiqc pureclip python markdown: 92%|████████████████████████████████████████████████Examining conflict for cutadapt piranha bowtie2 pygments umi_tools meme icount rseqc pymdown-extensions pureclip multiqc markdown: 92%|███████████████████████████████████████████████████████Examining conflict for cutadapt piranha bowtie2 pygments umi_tools meme icount rseqc pymdown-extensions pureclip multiqc markdown: 96%|███████████████████████████████████████████████████████Examining conflict for pureclip meme: 96%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for pureclip meme: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████Examining conflict for cutadapt bowtie2 samtools umi_tools pygments bedtools meme icount rseqc pymdown-extensions multiqc pureclip python markdown: 100%|██████████████████████████████████████Examining conflict for rseqc pureclip icount: : 26it [04:44, 15.13s/it] failed - /
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed -

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package pypy3.9 conflicts for:
bioconda::multiqc=1.9 -> click -> pypy3.9[version='7.3.11.|>=7.3.11|>=7.3.8|>=7.3.9|7.3.9.|7.3.8.']
bioconda::umi_tools=1.1.1 -> future -> pypy3.9[version='>=7.3.11|>=7.3.8|>=7.3.9']
bioconda::bowtie2=2.4.2 -> python[version='>=3.9,<3.10.0a0'] -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.']
conda-forge::pymdown-extensions=6.0 -> python -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.']
conda-forge::markdown=3.1.1 -> python -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.|>=7.3.9|>=7.3.8']
conda-forge::pygments=2.5.2 -> python -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.|>=7.3.9|>=7.3.8']
bioconda::rseqc=4.0.0 -> numpy -> pypy3.9[version='7.3.11.|>=7.3.11|>=7.3.9|>=7.3.8|7.3.9.|7.3.8.']
bioconda::icount=2.0.0 -> matplotlib -> pypy3.9[version='7.3.11.|>=7.3.11|>=7.3.9|>=7.3.8|7.3.9.|7.3.8.*']

Package libgcc-ng conflicts for:
bioconda::umi_tools=1.1.1 -> libgcc-ng[version='>=7.5.0|>=9.3.0']
bioconda::meme=5.1.1 -> expat[version='>=2.2.9,<2.3.0a0'] -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=4.9|>=12|>=9.4.0|>=11.2.0|>=7.2.0']
bioconda::cutadapt=3.0 -> libgcc-ng[version='>=7.5.0']
bioconda::samtools=1.11 -> ncurses[version='>=6.2,<6.3.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
conda-forge::pigz=2.3.4 -> libgcc-ng[version='>=7.3.0']
bioconda::subread=2.0.1 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.3.0']
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> libgcc-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=12|>=7.2.0|>=4.9|>=11.2.0']
bioconda::samtools=1.11 -> libgcc-ng[version='>=7.5.0']
bioconda::rseqc=4.0.0 -> libgcc-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.5.0']
bioconda::cutadapt=3.0 -> dnaio[version='>=0.4.2'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.3.0|>=7.2.0|>=4.9|>=11.2.0']
bioconda::preseq=2.0.3 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0']
bioconda::fastqc=0.11.9 -> fontconfig -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::preseq=2.0.3 -> gsl[version='>=2.6,<2.7.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.3.0|>=9.4.0|>=11.2.0|>=7.2.0']
bioconda::paraclu=9 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::piranha=1.2.1 -> libgcc-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
conda-forge::pymdown-extensions=6.0 -> python -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
conda-forge::python=3.7.3 -> libgcc-ng[version='>=7.3.0']
conda-forge::perl=5.26.2 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0']
bioconda::multiqc=1.9 -> matplotlib-base[version='>=2.1.1'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=11.2.0|>=4.9|>=7.2.0']
bioconda::bedtools=2.29.2 -> bzip2[version='>=1.0.8,<2.0a0'] -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=12|>=7.5.0|>=9.3.0|>=4.9|>=7.2.0']
bioconda::pureclip=1.3.1 -> bedtools -> libgcc-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=12|>=4.9']
conda-forge::pigz=2.3.4 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=7.5.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::piranha=1.2.1 -> gsl[version='>=2.7,<2.8.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.2.0|>=12']
conda-forge::pygments=2.5.2 -> python -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::rseqc=4.0.0 -> bx-python -> libgcc-ng[version='7.2.0.*|>=11.2.0|>=4.9|>=7.3.0|>=9.4.0|>=7.2.0']
conda-forge::python=3.7.3 -> bzip2[version='>=1.0.8,<2.0a0'] -> libgcc-ng[version='>=10.3.0|>=4.9|>=7.5.0|>=9.3.0|>=7.2.0|>=9.4.0|>=11.2.0|>=12']
conda-forge::markdown=3.1.1 -> python -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::bowtie2=2.4.2 -> perl -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=4.9|>=7.3.0|>=9.4.0|>=7.2.0|>=12']
bioconda::meme=5.1.1 -> libgcc-ng[version='>=7.3.0|>=7.5.0']
bioconda::bowtie2=2.4.2 -> libgcc-ng[version='>=7.5.0|>=9.3.0']
bioconda::umi_tools=1.1.1 -> matplotlib-base -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=7.3.0|>=11.2.0|>=4.9|>=7.2.0']
bioconda::paraclu=9 -> libgcc-ng[version='>=7.5.0']
bioconda::bedtools=2.29.2 -> libgcc-ng[version='>=7.3.0']
bioconda::subread=2.0.1 -> libzlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=11.2.0|>=12|>=7.5.0|>=4.9|>=7.2.0']

Package cutadapt conflicts for:
bioconda::icount=2.0.0 -> cutadapt[version='>=1.10']
bioconda|bioconda::cutadapt=3.0
bioconda::cutadapt=3.0

Package readline conflicts for:
bioconda::meme=5.1.1 -> python[version='>=3.8,<3.9.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.|7.0.']
conda-forge::python=3.7.3 -> readline[version='>=7.0,<8.0a0|>=8.0,<9.0a0']
conda-forge::markdown=3.1.1 -> python -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.|7.']
conda-forge::pygments=2.5.2 -> python -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.|7.']
bioconda::rseqc=4.0.0 -> python[version='>=3.10,<3.11.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.']
bioconda::cutadapt=3.0 -> python[version='>=3.6,<3.7.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|7.|>=8.1.2,<9.0a0|>=8.2,<9.0a0']
bioconda::icount=2.0.0 -> python[version='>=3'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.']
conda-forge::pymdown-extensions=6.0 -> python -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.|7.']
conda-forge::python=3.7.3 -> sqlite[version='>=3.30.1,<4.0a0'] -> readline[version='>=8.1,<9.0a0|>=8.1.2,<9.0a0']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.']
bioconda::umi_tools=1.1.1 -> python[version='>=3.8,<3.9.0a0'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.']
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.']

Package libpng conflicts for:
bioconda::icount=2.0.0 -> matplotlib -> libpng[version='>=1.6.23,<1.7|>=1.6.37,<1.7.0a0|>=1.6.36,<1.7.0a0|>=1.6.35,<1.7.0a0|>=1.6.34,<1.7.0a0|>=1.6.32,<1.7.0a0']
bioconda::multiqc=1.9 -> matplotlib-base[version='>=2.1.1'] -> libpng[version='>=1.6.35,<1.7.0a0|>=1.6.37,<1.7.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> libpng[version='>=1.6.21,<1.7|>=1.6.22,<1.6.31|>=1.6.32,<1.6.35|>=1.6.34,<1.7.0a0|>=1.6.35,<1.7.0a0|>=1.6.37,<1.7.0a0|>=1.6.28,<1.7|>=1.6.23,<1.7|>=1.6.32,<1.7.0a0|>=1.6.39,<1.7.0a0|>=1.6.38,<1.7.0a0']
bioconda::rseqc=4.0.0 -> r-base -> libpng[version='>=1.6.22,<1.6.31|>=1.6.32,<1.6.35|>=1.6.34,<1.7.0a0|>=1.6.35,<1.7.0a0|>=1.6.37,<1.7.0a0|>=1.6.38,<1.7.0a0|>=1.6.39,<1.7.0a0|>=1.6.28,<1.7|>=1.6.32,<1.7.0a0|>=1.6.27,<1.7']
bioconda::umi_tools=1.1.1 -> matplotlib-base -> libpng[version='>=1.6.35,<1.7.0a0|>=1.6.37,<1.7.0a0']

Package libgfortran4 conflicts for:
bioconda::preseq=2.0.3 -> openblas -> libgfortran4[version='>=7.5.0']
bioconda::rseqc=4.0.0 -> r-base -> libgfortran4[version='>=7.5.0']
bioconda::meme=5.1.1 -> openmpi[version='>=4.0.5,<4.1.0a0'] -> libgfortran4[version='>=7.5.0']
bioconda::umi_tools=1.1.1 -> scipy -> libgfortran4[version='>=7.5.0']
bioconda::piranha=1.2.1 -> openblas -> libgfortran4[version='>=7.5.0']

Package libxml2 conflicts for:
bioconda::meme=5.1.1 -> libxml2[version='>=2.9.10,<2.10.0a0']
bioconda::pureclip=1.3.1 -> meme -> libxml2[version='2.9.|>=2.9.10,<2.10.0a0|>=2.9.12,<2.10.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0']
bioconda::meme=5.1.1 -> libxslt[version='>=1.1.33,<2.0a0'] -> libxml2[version='>=2.10.3,<2.11.0a0|>=2.9.14,<2.11.0a0|>=2.9.12,<2.11.0a0|>=2.9.10,<2.11.0a0|>=2.9.9,<2.11.0a0|>=2.9.14,<2.10.0a0|>=2.9.8,<2.10.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> libxml2[version='2.9.|>=2.9.10,<2.11.0a0|>=2.9.12,<2.11.0a0|>=2.9.9,<2.11.0a0|>=2.9.8,<2.11.0a0|>=2.10.3,<2.11.0a0|>=2.9.14,<2.10.0a0|>=2.9.10,<2.10.0a0|>=2.9.8,<2.10.0a0|>=2.9.7,<2.10.0a0|>=2.9.4,<2.10.0a0']
bioconda::rseqc=4.0.0 -> r-base -> libxml2[version='2.9.*|>=2.10.3,<2.11.0a0|>=2.9.14,<2.11.0a0|>=2.9.12,<2.11.0a0|>=2.9.10,<2.11.0a0|>=2.9.9,<2.11.0a0|>=2.9.8,<2.11.0a0|>=2.9.9,<2.10.0a0|>=2.9.8,<2.10.0a0|>=2.9.7,<2.10.0a0|>=2.9.4,<2.10.0a0']

Package libstdcxx-ng conflicts for:
bioconda::rseqc=4.0.0 -> numpy -> libstdcxx-ng[version='7.2.0.*|>=10.3.0|>=12|>=9.4.0|>=7.3.0|>=4.9|>=11.2.0|>=7.5.0|>=9.3.0|>=7.2.0']
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> libstdcxx-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0|>=12|>=11.2.0']
bioconda::bedtools=2.29.2 -> libstdcxx-ng[version='>=7.3.0']
bioconda::meme=5.1.1 -> expat[version='>=2.2.9,<2.3.0a0'] -> libstdcxx-ng[version='>=10.3.0|>=7.3.0|>=9.3.0|>=7.5.0|>=4.9|>=12|>=9.4.0|>=11.2.0|>=7.2.0']
bioconda::multiqc=1.9 -> matplotlib-base[version='>=2.1.1'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=11.2.0|>=4.9|>=7.2.0']
bioconda::pureclip=1.3.1 -> bedtools -> libstdcxx-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
conda-forge::pygments=2.5.2 -> python -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0']
conda-forge::markdown=3.1.1 -> python -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0']
bioconda::fastqc=0.11.9 -> openjdk[version='>=8.0.144'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.3.0|>=7.5.0|>=7.3.0']
bioconda::piranha=1.2.1 -> bamtools[version='>=2.5.1,<2.5.2.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0']
conda-forge::python=3.7.3 -> libffi[version='>=3.2.1,<3.3.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.5.0']
bioconda::piranha=1.2.1 -> libstdcxx-ng[version='>=10.3.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0']
bioconda::cutadapt=3.0 -> python[version='>=3.6,<3.7.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0']
bioconda::paraclu=9 -> libstdcxx-ng[version='>=7.5.0']
bioconda::umi_tools=1.1.1 -> matplotlib-base -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=11.2.0|>=4.9|>=7.2.0']
bioconda::bowtie2=2.4.2 -> libstdcxx-ng[version='>=7.5.0|>=9.3.0']
bioconda::preseq=2.0.3 -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0']
conda-forge::python=3.7.3 -> libstdcxx-ng[version='>=7.3.0']
bioconda::samtools=1.11 -> ncurses[version='>=6.2,<6.3.0a0'] -> libstdcxx-ng[version='>=7.3.0|>=7.5.0']
bioconda::preseq=2.0.3 -> libgcc -> libstdcxx-ng[version='>=7.2.0']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.3.0|>=9.4.0|>=4.9|>=7.2.0']
conda-forge::pymdown-extensions=6.0 -> python -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0']

Package python_abi conflicts for:
conda-forge::pymdown-extensions=6.0 -> python -> python_abi[version='3.6|3.7|3.8.|3.8|3.9',build='_pypy36_pp73|_pypy37_pp73|_graalpy223_38_native|_pypy38_pp73|_pypy39_pp73']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> python_abi[version='3.6|3.7|3.8|3.8.|3.9',build='_pypy36_pp73|_pypy37_pp73|_graalpy223_38_native|_pypy38_pp73|_pypy39_pp73']
bioconda::rseqc=4.0.0 -> python_abi[version='3.10.|3.6.|3.9.|3.7.|3.8.',build='_cp310|_cp36m|_cp39|_cp37m|_cp38']
bioconda::cutadapt=3.0 -> python_abi[version='3.6.|3.8.|3.7.',build='_cp36m|_cp38|_cp37m']
bioconda::umi_tools=1.1.1 -> python_abi[version='3.6.|3.7.|3.8.',build='_cp36m|_cp37m|_cp38']
bioconda::meme=5.1.1 -> python_abi[version='2.7.|3.6.|3.7.|3.8.',build='_cp27mu|_cp36m|_cp37m|_cp38']
bioconda::meme=5.1.1 -> python[version='>=3.8,<3.9.0a0'] -> python_abi[version='3.6|3.7|3.8|3.8.',build='_pypy36_pp73|_pypy37_pp73|_graalpy223_38_native|_pypy38_pp73']
bioconda::piranha=1.2.1 -> python_abi=2.7[build=_cp27mu]
bioconda::umi_tools=1.1.1 -> future -> python_abi[version='2.7.|3.10.|3.9|3.9.|3.8|3.7|3.6|3.11.|3.8.',build='_cp311|_cp27mu|_pypy36_pp73|_pypy37_pp73|_cp39|_cp310|_pypy39_pp73|_pypy38_pp73|_graalpy223_38_native']
conda-forge::pygments=2.5.2 -> python -> python_abi[version='3.10.|3.6|3.7|3.8.|3.8|3.9|3.9.|3.7.|3.8.|3.11.|3.6.',build='_cp36m|_cp311|_cp310|_cp37m|_cp39|_pypy36_pp73|_pypy37_pp73|_graalpy223_38_native|_pypy38_pp73|_pypy39_pp73|_cp38']
conda-forge::markdown=3.1.1 -> python -> python_abi[version='3.10.|3.6|3.7|3.8.|3.8|3.9|3.9.|3.7.|3.8.|3.11.|3.6.',build='_cp36m|_cp311|_cp310|_cp37m|_cp39|_pypy36_pp73|_pypy37_pp73|_graalpy223_38_native|_pypy38_pp73|_pypy39_pp73|_cp38']
bioconda::multiqc=1.9 -> click -> python_abi[version='2.7.|3.10.|3.11.|3.8|3.8.|3.9.|3.9|3.7.|3.7|3.6|3.6.|3.8.',build='_graalpy223_38_native|_cp27mu|_cp36m|_pypy36_pp73|_cp37m|_cp310|_cp311|_cp39|_pypy38_pp73|_cp38|_pypy39_pp73|_pypy37_pp73']
bioconda::rseqc=4.0.0 -> bx-python -> python_abi[version='2.7.|3.8|3.9|3.11.|3.7|3.6|3.8.',build='_graalpy223_38_native|_pypy37_pp73|_cp311|_pypy39_pp73|_pypy38_pp73|_cp27mu|_pypy36_pp73']
bioconda::bowtie2=2.4.2 -> python_abi[version='3.6.|3.7.|3.8.|3.9.',build='_cp36m|_cp37m|_cp38|_cp39']
bioconda::pureclip=1.3.1 -> meme -> python_abi[version='2.7.|3.10.|3.6.|3.7.|3.9.|3.8.',build='_cp39|_cp310|_cp36m|_cp37m|_cp27mu|_cp38']
bioconda::cutadapt=3.0 -> dnaio[version='>=0.4.2'] -> python_abi[version='3.10.|3.9.|3.6|3.11.|3.7|3.8|3.8.',build='_graalpy223_38_native|_pypy38_pp73|_pypy37_pp73|_cp311|_pypy36_pp73|_cp310|_cp39']
bioconda::icount=2.0.0 -> cutadapt[version='>=1.10'] -> python_abi[version='2.7.|3.10.|3.7.|3.8.|3.9.|3.6.|3.9|3.11.|3.8|3.7|3.6|3.8.',build='_graalpy223_38_native|_pypy36_pp73|_pypy37_pp73|_pypy38_pp73|_cp311|_cp36m|_cp310|_cp37m|_cp38|_cp39|_pypy39_pp73|*_cp27mu']

Package libuuid conflicts for:
conda-forge::markdown=3.1.1 -> python -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0|>=2.38.1,<3.0a0']
bioconda::rseqc=4.0.0 -> python[version='>=3.10,<3.11.0a0'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0']
bioconda::umi_tools=1.1.1 -> python[version='>=3.8,<3.9.0a0'] -> libuuid[version='>=2.32.1,<3.0a0']
bioconda::icount=2.0.0 -> python[version='>=3'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0|>=2.38.1,<3.0a0']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> libuuid[version='>=2.32.1,<3.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0']
conda-forge::pygments=2.5.2 -> python -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0|>=2.38.1,<3.0a0']
bioconda::meme=5.1.1 -> python[version='>=3.8,<3.9.0a0'] -> libuuid[version='>=2.32.1,<3.0a0']
conda-forge::pymdown-extensions=6.0 -> python -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0|>=2.38.1,<3.0a0']
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0|>=2.32.1,<3.0a0|>=2.38.1,<3.0a0']
bioconda::cutadapt=3.0 -> python[version='>=3.8,<3.9.0a0'] -> libuuid[version='>=2.32.1,<3.0a0']

Package importlib-metadata conflicts for:
bioconda::multiqc=1.9 -> click -> importlib-metadata[version='>=4.4']
bioconda::icount=2.0.0 -> sphinx[version='>=1.4'] -> importlib-metadata[version='>=4.4|>=4.8']
conda-forge::pymdown-extensions=6.0 -> markdown[version='>=3.0.1'] -> importlib-metadata[version='>=4.4']

Package tzdata conflicts for:
conda-forge::pymdown-extensions=6.0 -> python -> tzdata
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> tzdata
bioconda::icount=2.0.0 -> python[version='>=3'] -> tzdata
conda-forge::markdown=3.1.1 -> python -> tzdata
bioconda::bowtie2=2.4.2 -> python[version='>=3.9,<3.10.0a0'] -> tzdata
bioconda::rseqc=4.0.0 -> python[version='>=3.10,<3.11.0a0'] -> tzdata
conda-forge::pygments=2.5.2 -> python -> tzdata

Package bedtools conflicts for:
bioconda|bioconda::bedtools=2.29.2
bioconda::pureclip=1.3.1 -> bedtools
bioconda::bedtools=2.29.2
bioconda::icount=2.0.0 -> pybedtools -> bedtools
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0']

Package certifi conflicts for:
bioconda::umi_tools=1.1.1 -> matplotlib-base -> certifi[version='>=2020.06.20']
bioconda::multiqc=1.9 -> matplotlib-base[version='>=2.1.1'] -> certifi[version='>=2016.09|>=2016.9.26|>=2017.4.17|>=2020.06.20']
conda-forge::pygments=2.5.2 -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
conda-forge::markdown=3.1.1 -> setuptools[version='>=36'] -> certifi[version='>=2016.09|>=2016.9.26']

Package star conflicts for:
bioconda::star=2.6.1d
bioconda::icount=2.0.0 -> star
bioconda|bioconda::star=2.6.1d

Package gsl conflicts for:
bioconda::preseq=2.0.3 -> gsl[version='1.16.|2.2.|>=2.2.1,<2.3.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0']
bioconda::rseqc=4.0.0 -> r-base -> gsl[version='>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.5,<2.6.0a0|>=2.6,<2.7.0a0|>=2.7,<2.8.0a0']
bioconda::piranha=1.2.1 -> gsl[version='1.16.|2.2.|>=2.2.1,<2.3.0a0|>=2.4,<2.5.0a0|>=2.6,<2.7.0a0|>=2.7,<2.8.0a0']

Package setuptools conflicts for:
bioconda::multiqc=1.9 -> setuptools
bioconda::rseqc=4.0.0 -> bx-python -> setuptools
bioconda::umi_tools=1.1.1 -> matplotlib-base -> setuptools[version='<60.0.0']
bioconda::multiqc=1.9 -> markdown -> setuptools[version='>=36']
conda-forge::markdown=3.1.1 -> setuptools[version='>=36']
conda-forge::pymdown-extensions=6.0 -> markdown[version='>=3.0.1'] -> setuptools[version='>=36']
conda-forge::python=3.7.3 -> pip -> setuptools
bioconda::icount=2.0.0 -> matplotlib -> setuptools[version='<60.0.0']
conda-forge::pygments=2.5.2 -> setuptools

Package pygments conflicts for:
conda-forge::pygments=2.5.2
bioconda::icount=2.0.0 -> sphinx[version='>=1.4'] -> pygments[version='>2.0|>=2.0|>=2.12|>=2.13']
conda-forge|conda-forge::pygments=2.5.2

Package bcftools conflicts for:
bioconda::icount=2.0.0 -> pysam -> bcftools[version='1.3|1.3.1.|1.3.1|1.5.|1.6.|1.6|1.7.|1.9.|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3,<1.4|>=1.3']
bioconda::rseqc=4.0.0 -> pysam -> bcftools[version='1.3|1.3.1.|1.3.1|1.5.|1.6.|1.6|1.7.|1.9.|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3,<1.4|>=1.3']

Package ncurses conflicts for:
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
bioconda::icount=2.0.0 -> python[version='>=3'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
conda-forge::markdown=3.1.1 -> python -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
bioconda::cutadapt=3.0 -> python[version='>=3.6,<3.7.0a0'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.|>=6.3,<7.0a0|>=6.4,<7.0a0']
bioconda::meme=5.1.1 -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
conda-forge::pygments=2.5.2 -> python -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
conda-forge::python=3.7.3 -> ncurses[version='>=6.1,<7.0.0a0']
bioconda::rseqc=4.0.0 -> python[version='>=3.10,<3.11.0a0'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|6.0.|>=6.0,<7.0a0|>=5.9*|>=5.9.']
bioconda::umi_tools=1.1.1 -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
conda-forge::pymdown-extensions=6.0 -> python -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.2,<7.0.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']
bioconda::samtools=1.11 -> ncurses[version='>=6.2,<6.3.0a0']
conda-forge::python=3.7.3 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='5.9.|>=6.1,<7.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.2,<7.0a0|>=6.4,<7.0a0|>=6.0,<7.0a0|6.0.*']

Package numpy-base conflicts for:
bioconda::multiqc=1.9 -> numpy -> numpy-base[version='1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.17.2.|1.17.3.|1.17.4.|1.18.1.|1.18.5.|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.5|1.19.5|1.19.5|1.19.5|1.19.5|1.19.5|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.23.1|1.23.1|1.23.1|1.23.1|1.23.1|1.23.1|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.4|1.23.4|1.23.4|1.23.4|1.23.4|1.23.4|1.23.5|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|>=1.9.3,<2.0a0|1.17.0|1.17.0|1.17.0|1.17.0',build='py37h2f8d375_0|py37h2b20989_6|py27hdbf6ddf_6|py36hdbf6ddf_6|py27h2b20989_7|py35h2b20989_7|py27h2b20989_7|py27hdbf6ddf_7|py36h2b20989_8|py37h2b20989_8|py27h2b20989_8|py35hdbf6ddf_8|py35h2b20989_8|py35h7cdd4dd_9|py37h7cdd4dd_9|py36h3dfced4_9|py35h3dfced4_9|py37h81de0dd_9|py27h74e8950_9|py37h74e8950_9|py27h81de0dd_9|py37h81de0dd_10|py36h81de0dd_10|py35h81de0dd_10|py37h2f8d375_10|py36h2f8d375_10|py27h2f8d375_10|py35h2f8d375_10|py27h2f8d375_11|py36h2f8d375_11|py36hde5b4d6_11|py37hde5b4d6_11|py37h2f8d375_12|py27h2f8d375_12|py36h0ea5e3f_1|py27h0ea5e3f_1|py35h0ea5e3f_1|py35h9be14a7_1|py27h2b20989_0|py27hdbf6ddf_0|py35hdbf6ddf_0|py27h2b20989_0|py36hdbf6ddf_0|py27hdbf6ddf_0|py35hdbf6ddf_0|py36h2b20989_1|py37hdbf6ddf_1|py27h2b20989_2|py37h2b20989_2|py27hdbf6ddf_2|py37hdbf6ddf_2|py36hdbf6ddf_2|py36h2b20989_3|py27h2b20989_3|py27hdbf6ddf_3|py37h2b20989_4|py36h2b20989_4|py36hdbf6ddf_4|py35hdbf6ddf_4|py27h81de0dd_4|py36h81de0dd_4|py36h2f8d375_5|py37h2f8d375_5|py36hde5b4d6_5|py36h7cdd4dd_0|py37h7cdd4dd_0|py35h7cdd4dd_0|py36h3dfced4_0|py35h3dfced4_0|py35h74e8950_0|py36h74e8950_0|py37h74e8950_0|py36h81de0dd_0|py27h81de0dd_0|py37h81de0dd_0|py35h2f8d375_0|py37h81de0dd_0|py27h81de0dd_0|py35h81de0dd_0|py36h81de0dd_0|py27h81de0dd_1|py37h81de0dd_1|py27h81de0dd_0|py36h81de0dd_0|py37h81de0dd_0|py36h81de0dd_0|py27h81de0dd_0|py27hde5b4d6_0|py37h2f8d375_0|py36hde5b4d6_0|py37h2f8d375_1|py27h2f8d375_1|py36h2f8d375_1|py36hde5b4d6_1|py36hde5b4d6_0|py27h2f8d375_1|py36hde5b4d6_1|py36hde5b4d6_0|py27hde5b4d6_0|py36hde5b4d6_0|py36hde5b4d6_0|py27hde5b4d6_0|py36hde5b4d6_0|py37h2f8d375_0|py36hde5b4d6_0|py39hfb011de_1|py39h76555f2_1|py37h41b4c56_3|py36hdc34a94_3|py37ha8aedfd_4|py38ha8aedfd_4|py37h73d599e_4|py36h75fe3a5_0|py38h75fe3a5_0|py37h75fe3a5_0|py36h75fe3a5_0|py38hfa32c7d_0|py39h2ae0177_0|py37h4c65ebe_1|py37h21a3de8_1|py38h21a3de8_1|py39h622ebfc_4|py37h34387ca_0|py38h7d8b39e_0|py39h7d8b39e_0|py39he2ba247_0|py37h74d4b33_0|py39h74d4b33_0|py38h74d4b33_0|py38h39b7dee_0|py37h39b7dee_0|py38h79a1101_0|py37h2b8c604_0|py39h2b8c604_0|py310h2b8c604_0|py310h79a1101_0|py39hb8be1f0_1|py38hb8be1f0_1|py37hb8be1f0_1|py310h9585f30_1|py310hf2716ce_2|py37hb8be1f0_2|py310h9585f30_2|py39hf524024_2|py37hf524024_2|py38h1e6e340_3|py39h1e6e340_3|py38ha15fc14_3|py310hcba007f_3|py39ha15fc14_3|py310h9585f30_0|py310hf2716ce_0|py311h0ff3221_1|py39h1e6e340_0|py38h1e6e340_0|py310h375b286_0|py39ha15fc14_0|py310hcba007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bioconda::rseqc=4.0.0 -> numpy -> 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bioconda::umi_tools=1.1.1 -> numpy[version='>=1.7'] -> 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bioconda::icount=2.0.0 -> numpy -> 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Package pypy3.7 conflicts for:
bioconda::umi_tools=1.1.1 -> future -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.7|>=7.3.5|>=7.3.4']
conda-forge::pymdown-extensions=6.0 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.']
bioconda::meme=5.1.1 -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.']
conda-forge::pygments=2.5.2 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.7|>=7.3.5|>=7.3.3']
bioconda::multiqc=1.9 -> click -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
bioconda::rseqc=4.0.0 -> numpy -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
bioconda::icount=2.0.0 -> matplotlib -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
bioconda::bowtie2=2.4.2 -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.']
conda-forge::markdown=3.1.1 -> python -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.7|>=7.3.5|>=7.3.3']
bioconda::cutadapt=3.0 -> xopen[version='>=1.0.0'] -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']

Package markdown conflicts for:
conda-forge::markdown=3.1.1
bioconda::multiqc=1.9 -> markdown
conda-forge|conda-forge::markdown=3.1.1
conda-forge::pymdown-extensions=6.0 -> markdown[version='>=3.0.1']

Package yaml conflicts for:
bioconda::multiqc=1.9 -> pyyaml[version='>=4'] -> yaml[version='>=0.1.7,<0.2.0a0|>=0.2.2,<0.3.0a0|>=0.2.5,<0.3.0a0']
bioconda::pureclip=1.3.1 -> meme -> yaml[version='>=0.1.7,<0.2.0a0|>=0.2.2,<0.3.0a0|>=0.2.4,<0.3.0a0|>=0.2.5,<0.3.0a0']
bioconda::meme=5.1.1 -> yaml[version='>=0.2.4,<0.3.0a0|>=0.2.5,<0.3.0a0']

Package libdeflate conflicts for:
bioconda::rseqc=4.0.0 -> pysam -> libdeflate[version='>=1.0,<1.1.0a0|>=1.10,<1.11.0a0|>=1.13,<1.14.0a0|>=1.9,<1.10.0a0|>=1.7,<1.8.0a0|>=1.6,<1.7.0a0|>=1.5,<1.6.0a0|>=1.3,<1.4.0a0']
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> libdeflate[version='>=1.0,<1.1.0a0|>=1.13,<1.14.0a0|>=1.10,<1.11.0a0|>=1.9,<1.10.0a0|>=1.7,<1.8.0a0|>=1.6,<1.7.0a0|>=1.5,<1.6.0a0|>=1.3,<1.4.0a0']
bioconda::umi_tools=1.1.1 -> pysam[version='>=0.16.0.1'] -> libdeflate[version='>=1.10,<1.11.0a0|>=1.13,<1.14.0a0|>=1.9,<1.10.0a0|>=1.7,<1.8.0a0|>=1.6,<1.7.0a0']
bioconda::pureclip=1.3.1 -> bedtools -> libdeflate[version='>=1.0,<1.1.0a0']
bioconda::samtools=1.11 -> htslib[version='>=1.11,<1.12.0a0'] -> libdeflate[version='>=1.6,<1.7.0a0|>=1.7,<1.8.0a0']

Package ca-certificates conflicts for:
bioconda::meme=5.1.1 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
conda-forge::python=3.7.3 -> openssl[version='>=1.1.1a,<1.1.2a'] -> ca-certificates
conda-forge::pygments=2.5.2 -> python -> ca-certificates
conda-forge::markdown=3.1.1 -> python -> ca-certificates
conda-forge::pymdown-extensions=6.0 -> python -> ca-certificates

Package libcurl conflicts for:
bioconda::rseqc=4.0.0 -> pybigwig -> libcurl[version='>=7.58.0,<8.0a0|>=7.60.0,<8.0a0|>=7.61.0,<8.0a0|>=7.61.1,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0|>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.81.0,<8.0a0|>=7.83.1,<8.0a0|>=7.87.0,<8.0a0|>=7.86.0,<8.0a0|>=7.82.0,<8.0a0|>=7.79.1,<8.0a0|>=7.88.1,<8.0a0|>=7.85.0,<8.0a0|>=7.80.0,<8.0a0|>=7.78.0,<8.0a0|>=7.77.0,<8.0a0|>=7.76.1,<8.0a0|>=7.71.0,<8.0a0|>=7.62.0,<8.0a0']
bioconda::umi_tools=1.1.1 -> pysam[version='>=0.16.0.1'] -> libcurl[version='>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.79.1,<8.0a0|>=7.81.0,<8.0a0|>=7.82.0,<8.0a0|>=7.83.1,<8.0a0|>=7.86.0,<8.0a0|>=7.87.0,<8.0a0']
bioconda::icount=2.0.0 -> pysam -> libcurl[version='>=7.69.1,<8.0a0|>=7.71.1,<8.0a0|>=7.75.0,<8.0a0|>=7.79.1,<8.0a0|>=7.81.0,<8.0a0|>=7.82.0,<8.0a0|>=7.83.1,<8.0a0|>=7.86.0,<8.0a0|>=7.87.0,<8.0a0']
bioconda::samtools=1.11 -> htslib[version='>=1.11,<1.12.0a0'] -> libcurl[version='>=7.71.1,<8.0a0']

Package python conflicts for:
bioconda::multiqc=1.9 -> python[version='>=3.6']
bioconda::rseqc=4.0.0 -> python[version='>=3.10,<3.11.0a0|>=3.6,<3.7.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
bioconda::umi_tools=1.1.1 -> future -> python[version='2.7.|3.4.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|>=3.11,<3.12.0a0|>=3.7.1,<3.8.0a0|3.8.|3.7.']
bioconda::rseqc=4.0.0 -> bx-python -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.11,<3.12.0a0|3.4.|>=3.7|>=3.6|>=3|<3.0.0|3.10.|3.9.|3.7.|3.8.']
bioconda::multiqc=1.9 -> click -> python[version='2.7.|3.5.|3.6.|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.8|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|3.4.|>=3|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7|>=3.5|>=3.7,<4.0|>=3.6,<4.0']
bioconda::cutadapt=3.0 -> python[version='>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0']
conda-forge|conda-forge::python=3.7.3
conda-forge::python=3.7.3
bioconda::piranha=1.2.1 -> python_abi=2.7[build=_cp27mu] -> python=2.7
conda-forge::pygments=2.5.2 -> setuptools -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.7|>=3.8|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.11,<3.12.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.']
bioconda::umi_tools=1.1.1 -> python[version='>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
bioconda::bowtie2=2.4.2 -> python[version='>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
conda-forge::markdown=3.1.1 -> python
conda-forge::markdown=3.1.1 -> setuptools[version='>=36'] -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.7|>=3.8|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.11,<3.12.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
conda-forge::pygments=2.5.2 -> python
bioconda::cutadapt=3.0 -> dnaio[version='>=0.4.2'] -> python[version='3.6.|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.11,<3.12.0a0|3.8.|3.7.']
bioconda::icount=2.0.0 -> cutadapt[version='>=1.10'] -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|3.4.|>=3.11,<3.12.0a0|>=3.7|>=3.5|>=3.7.1,<3.8.0a0|<3.0.0|>=3.8|>=3.6']
bioconda::pureclip=1.3.1 -> meme -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|3.4.']
conda-forge::pymdown-extensions=6.0 -> markdown[version='>=3.0.1'] -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.5|>=3.6|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0']
bioconda::bowtie2=2.4.2 -> python_abi=3.8[build=_cp38] -> python[version='3.6.|3.7.|3.8.|3.9.']
conda-forge::pymdown-extensions=6.0 -> python
bioconda::icount=2.0.0 -> python[version='>=3.6,<3.7.0a0|>=3|>=3.5,<3.6.0a0']
bioconda::meme=5.1.1 -> python_abi=3.8[build=_cp38] -> python[version='2.7.|3.6.|3.7.|3.8.*']
bioconda::meme=5.1.1 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']

Package libzlib conflicts for:
bioconda::piranha=1.2.1 -> bamtools[version='>=2.5.1,<2.5.2.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0']
bioconda::subread=2.0.1 -> libzlib[version='>=1.2.11,<1.3.0a0']
bioconda::preseq=2.0.3 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
conda-forge::python=3.7.3 -> sqlite[version='>=3.30.1,<4.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
conda-forge::pygments=2.5.2 -> python -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::rseqc=4.0.0 -> bx-python -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::subread=2.0.1 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
bioconda::umi_tools=1.1.1 -> pysam[version='>=0.16.0.1'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::samtools=1.11 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
conda-forge::markdown=3.1.1 -> python -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
conda-forge::pigz=2.3.4 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
conda-forge::pymdown-extensions=6.0 -> python -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::paraclu=9 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
bioconda::bedtools=2.29.2 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
bioconda::meme=5.1.1 -> libxml2[version='>=2.9.10,<2.10.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0',build='h166bdaf_1014|h166bdaf_0|h166bdaf_1|h166bdaf_2|h166bdaf_3|h166bdaf_4|h36c2ea0_1013|h36c2ea0_1012']
bioconda::cutadapt=3.0 -> python[version='>=3.6,<3.7.0a0'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0']
bioconda::pureclip=1.3.1 -> bedtools -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0']
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0']

Package gdbm conflicts for:
bioconda::bowtie2=2.4.2 -> perl -> gdbm[version='>=1.18|>=1.18,<1.19.0a0']
bioconda::fastqc=0.11.9 -> perl -> gdbm[version='>=1.18|>=1.18,<1.19.0a0']

Package pigz conflicts for:
conda-forge::pigz=2.3.4
bioconda::cutadapt=3.0 -> pigz
bioconda::icount=2.0.0 -> cutadapt[version='>=1.10'] -> pigz

Package xz conflicts for:
bioconda::pureclip=1.3.1 -> bedtools -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
bioconda::samtools=1.11 -> htslib[version='>=1.11,<1.12.0a0'] -> xz[version='>=5.2.5,<5.3.0a0']
bioconda::bedtools=2.29.2 -> xz[version='>=5.2.4,<5.3.0a0']
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bioconda::meme=5.1.1 -> libxml2[version='>=2.9.10,<2.10.0a0'] -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.4,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<5.3.0a0|>=5.2.3,<6.0a0']
bioconda::cutadapt=3.0 -> python[version='>=3.6,<3.7.0a0'] -> xz[version='5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0|>=5.2.6,<6.0a0|>=5.2.10,<6.0a0']
bioconda::bowtie2=2.4.2 -> python[version='>=3.8,<3.9.0a0'] -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<5.3.0a0|>=5.2.8,<6.0a0|>=5.2.3,<6.0a0']
conda-forge::pygments=2.5.2 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bioconda::umi_tools=1.1.1 -> pysam[version='>=0.16.0.1'] -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<5.3.0a0|>=5.2.3,<6.0a0']
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
conda-forge::python=3.7.3 -> xz[version='>=5.2.4,<5.3.0a0']
conda-forge::markdown=3.1.1 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
conda-forge::pymdown-extensions=6.0 -> python -> xz[version='5.0.|5.2.|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bioconda::rseqc=4.0.0 -> pysam -> xz[version='5.2.|>=5.2.10,<6.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.3,<5.3.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0']
bioconda::meme=5.1.1 -> xz[version='>=5.2.5,<5.3.0a0']

Package libexpat conflicts for:
conda-forge::pymdown-extensions=6.0 -> python -> libexpat[version='>=2.5.0,<3.0a0']
bioconda::multiqc=1.9 -> python[version='>=3.6'] -> libexpat[version='>=2.5.0,<3.0a0']
conda-forge::markdown=3.1.1 -> python -> libexpat[version='>=2.5.0,<3.0a0']
conda-forge::pygments=2.5.2 -> python -> libexpat[version='>=2.5.0,<3.0a0']
bioconda::icount=2.0.0 -> python[version='>=3'] -> libexpat[version='>=2.5.0,<3.0a0']

Package pysam conflicts for:
bioconda::icount=2.0.0 -> pybedtools -> pysam[version='>=0.16|>=0.8.1']
bioconda::umi_tools=1.1.1 -> pysam[version='>=0.16.0.1']
bioconda::icount=2.0.0 -> pysam
bioconda::rseqc=4.0.0 -> pysam

Package packaging conflicts for:
bioconda::icount=2.0.0 -> sphinx[version='>=1.4'] -> packaging[version='>=21.0']
bioconda::umi_tools=1.1.1 -> matplotlib-base -> packaging[version='>=20.0']
bioconda::multiqc=1.9 -> matplotlib-base[version='>=2.1.1'] -> packaging[version='>=20.0']

Package expat conflicts for:
bioconda::pureclip=1.3.1 -> meme -> expat[version='>=2.2.10,<2.3.0a0|>=2.4.2,<3.0a0|>=2.4.3,<3.0a0|>=2.4.6,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<2.3.0a0|>=2.2.5,<2.3.0a0']
bioconda::meme=5.1.1 -> expat[version='>=2.2.9,<2.3.0a0']
bioconda::meme=5.1.1 -> perl-xml-parser -> expat[version='2.2.*|>=2.2.5,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.5,<2.3.0a0|>=2.4.9,<3.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> expat[version='>=2.4.6,<3.0a0|>=2.4.7,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0']

Package libgfortran5 conflicts for:
bioconda::preseq=2.0.3 -> openblas -> libgfortran5[version='>=10.3.0|>=10.4.0|>=9.4.0|>=9.3.0']
bioconda::rseqc=4.0.0 -> numpy -> libgfortran5[version='>=10.3.0|>=10.4.0|>=11.2.0|>=11.3.0|>=9.4.0|>=9.3.0']
bioconda::umi_tools=1.1.1 -> numpy[version='>=1.7'] -> libgfortran5[version='>=10.3.0|>=10.4.0|>=11.2.0|>=11.3.0|>=9.4.0|>=9.3.0']
bioconda::icount=2.0.0 -> numpy -> libgfortran5[version='>=11.2.0']
bioconda::multiqc=1.9 -> numpy -> libgfortran5[version='>=11.2.0']
bioconda::meme=5.1.1 -> openmpi[version='>=4.0.5,<4.1.0a0'] -> libgfortran5[version='>=9.3.0']
bioconda::piranha=1.2.1 -> openblas -> libgfortran5[version='>=10.3.0|>=10.4.0|>=9.4.0|>=9.3.0']

Package libopenblas conflicts for:
bioconda::multiqc=1.9 -> numpy -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.20,<1.0a0|>=0.3.3,<1.0a0']
bioconda::preseq=2.0.3 -> gsl[version='>=2.6,<2.7.0a0'] -> libopenblas[version='0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.13|0.3.13|0.3.15|0.3.15|0.3.15|0.3.15|0.3.16|0.3.16|0.3.17|0.3.17|0.3.17|0.3.17|0.3.18|0.3.18|0.3.20|0.3.20|0.3.20|0.3.20|0.3.21|0.3.21|0.3.21|0.3.21|0.3.21|0.3.21|0.3.21|>=0.3.3,<1.0a0|0.3.9|0.3.8|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.6|0.3.6|0.3.6|0.3.6|0.3.21|0.3.20|0.3.20|0.3.18|0.3.17|0.3.13|0.3.6|0.3.6|0.3.6|0.3.3|0.3.3|0.3.3|>=0.3.2,<0.3.3.0a0|>=0.2.20,<0.2.21.0a0',build='h5a2b251_2|h5a2b251_2|hf726d26_1|hf726d26_0|h6e990d7_3|h6e990d7_4|h6e990d7_6|h6e990d7_0|h6e990d7_3|h5ec1e0e_4|h5ec1e0e_7|h5ec1e0e_0|openmp_h709eae2_1|pthreads_hb3c22a3_1|openmp_h709eae2_3|pthreads_hb3c22a3_4|openmp_h709eae2_4|openmp_h709eae2_5|openmp_h59f9010_0|openmp_h709eae2_1|pthreads_h8fe5266_0|pthreads_h8fe5266_0|openmp_h3d5035f_1|pthreads_h8fe5266_1|openmp_h3d5035f_1|openmp_h74cd887_3|pthreads_h78a6416_3|openmp_h74cd887_2|pthreads_h78a6416_2|pthreads_h78a6416_1|pthreads_h78a6416_0|openmp_h74cd887_0|openmp_h74cd887_1|pthreads_h78a6416_1|openmp_h74cd887_0|pthreads_h78a6416_0|pthreads_h8fe5266_0|openmp_h3d5035f_0|pthreads_h8fe5266_0|openmp_h3d5035f_0|openmp_h3d5035f_0|pthreads_h8fe5266_0|pthreads_h8fe5266_1|openmp_h3d5035f_0|openmp_h3d5035f_0|pthreads_h4812303_1|openmp_h59f9010_1|pthreads_hb3c22a3_1|openmp_h709eae2_0|pthreads_hb3c22a3_0|pthreads_h4812303_0|pthreads_hb3c22a3_5|pthreads_h4812303_5|openmp_h59f9010_5|pthreads_hb3c22a3_3|pthreads_hb3c22a3_2|openmp_h709eae2_2|h5ec1e0e_0|h5ec1e0e_0|h5ec1e0e_6|h5ec1e0e_5|h6e990d7_2|h6e990d7_1|h6e990d7_5|h043d6bf_0|h043d6bf_1|h043d6bf_0|h4367d64_0|h5a2b251_0|h5a2b251_1|h5a2b251_0|h5a2b251_3|h5a2b251_1']
bioconda::umi_tools=1.1.1 -> numpy[version='>=1.7'] -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.20,<1.0a0|>=0.3.3,<1.0a0|>=0.3.21,<1.0a0']
bioconda::icount=2.0.0 -> numpy -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.20,<1.0a0|>=0.3.3,<1.0a0']
bioconda::rseqc=4.0.0 -> numpy -> libopenblas[version='>=0.2.20,<0.2.21.0a0|>=0.3.2,<0.3.3.0a0|>=0.3.20,<1.0a0|>=0.3.3,<1.0a0']
bioconda::piranha=1.2.1 -> gsl[version='>=2.7,<2.8.0a0'] -> libopenblas[version='0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.10|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.12|0.3.13|0.3.13|0.3.15|0.3.15|0.3.15|0.3.15|0.3.16|0.3.16|0.3.17|0.3.17|0.3.17|0.3.17|0.3.18|0.3.18|0.3.20|0.3.20|0.3.20|0.3.20|0.3.21|0.3.21|0.3.21|0.3.21|0.3.21|0.3.21|0.3.21|>=0.2.20,<0.2.21.0a0|>=0.3.20,<1.0a0|>=0.3.3,<1.0a0|0.3.9|0.3.8|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.7|0.3.6|0.3.6|0.3.6|0.3.6|0.3.21|0.3.20|0.3.20|0.3.18|0.3.17|0.3.13|0.3.6|0.3.6|0.3.6|0.3.3|0.3.3|0.3.3|>=0.3.2,<0.3.3.0a0',build='h5a2b251_2|h5a2b251_2|hf726d26_1|hf726d26_0|h6e990d7_3|h6e990d7_4|h6e990d7_6|h6e990d7_0|h6e990d7_3|h5ec1e0e_4|h5ec1e0e_7|h5ec1e0e_0|openmp_h709eae2_1|pthreads_hb3c22a3_1|openmp_h709eae2_3|pthreads_hb3c22a3_4|openmp_h709eae2_4|openmp_h709eae2_5|openmp_h59f9010_0|openmp_h709eae2_1|pthreads_h8fe5266_0|pthreads_h8fe5266_0|openmp_h3d5035f_1|pthreads_h8fe5266_1|openmp_h3d5035f_1|openmp_h74cd887_3|pthreads_h78a6416_3|openmp_h74cd887_2|pthreads_h78a6416_2|pthreads_h78a6416_1|pthreads_h78a6416_0|openmp_h74cd887_0|openmp_h74cd887_1|pthreads_h78a6416_1|openmp_h74cd887_0|pthreads_h78a6416_0|pthreads_h8fe5266_0|openmp_h3d5035f_0|pthreads_h8fe5266_0|openmp_h3d5035f_0|openmp_h3d5035f_0|pthreads_h8fe5266_0|pthreads_h8fe5266_1|openmp_h3d5035f_0|openmp_h3d5035f_0|pthreads_h4812303_1|openmp_h59f9010_1|pthreads_hb3c22a3_1|openmp_h709eae2_0|pthreads_hb3c22a3_0|pthreads_h4812303_0|pthreads_hb3c22a3_5|pthreads_h4812303_5|openmp_h59f9010_5|pthreads_hb3c22a3_3|pthreads_hb3c22a3_2|openmp_h709eae2_2|h5ec1e0e_0|h5ec1e0e_0|h5ec1e0e_6|h5ec1e0e_5|h6e990d7_2|h6e990d7_1|h6e990d7_5|h043d6bf_0|h043d6bf_1|h043d6bf_0|h4367d64_0|h5a2b251_0|h5a2b251_1|h5a2b251_0|h5a2b251_3|h5a2b251_1']

Package colorama conflicts for:
bioconda::icount=2.0.0 -> sphinx[version='>=1.4'] -> colorama[version='>=0.3.5|>=0.4.5']
bioconda::multiqc=1.9 -> click -> colorama

Package icu conflicts for:
bioconda::multiqc=1.9 -> matplotlib-base[version='>=2.1.1'] -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0']
bioconda::icount=2.0.0 -> matplotlib -> icu[version='>=58.2,<59.0a0']
bioconda::rseqc=4.0.0 -> r-base -> icu[version='54.|56.|58.|>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0|>=69.1,<70.0a0|>=70.1,<71.0a0|>=72.1,<73.0a0']
bioconda::meme=5.1.1 -> libxml2[version='>=2.9.10,<2.10.0a0'] -> icu[version='69.|>=69.1,<70.0a0|>=70.1,<71.0a0|>=68.1,<69.0a0|>=67.1,<68.0a0|>=58.2,<59.0a0']
bioconda::umi_tools=1.1.1 -> matplotlib-base -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0']
bioconda::meme=5.1.1 -> icu[version='>=64.2,<65.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> icu[version='58.*|>=58.2,<59.0a0|>=64.2,<65.0a0|>=67.1,<68.0a0|>=68.1,<69.0a0']
bioconda::pureclip=1.3.1 -> meme -> icu[version='>=58.2,<59.0a0|>=64.2,<65.0a0|>=68.1,<69.0a0|>=68.2,<69.0a0|>=69.1,<70.0a0']

Package libgcc conflicts for:
bioconda::umi_tools=1.1.1 -> scipy -> libgcc
bioconda::rseqc=4.0.0 -> bx-python -> libgcc
bioconda::preseq=2.0.3 -> libgcc
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> libgcc
bioconda::pureclip=1.3.1 -> bedtools -> libgcc
bioconda::piranha=1.2.1 -> libgcc
bioconda::meme=5.1.1 -> ghostscript -> libgcc

Package meme conflicts for:
bioconda::meme=5.1.1
bioconda::pureclip=1.3.1 -> meme
bioconda|bioconda::meme=5.1.1

Package perl conflicts for:
bioconda::fastqc=0.11.9 -> perl
bioconda::pureclip=1.3.1 -> meme -> perl[version='5.22.0.|>=5.26.2,<5.26.3.0a0|>=5.32.1,<5.33.0a0',build=_perl5]
conda-forge::perl=5.26.2
conda-forge|conda-forge::perl=5.26.2
bioconda::meme=5.1.1 -> perl-cgi -> perl[version='5.22.0.|>=5.22.0,<5.23.0|>=5.26.2,<5.27.0a0|>=5.32.1,<5.33.0a0|>=5.32.1,<6.0a0|>=5.32.1,<5.32.2.0a0|>=5.32.1,<5.32.2.0a0|5.22.2.1|>=5.22.0.1,<5.23.0a0|>=5.22,<6.0',build=_perl5]
bioconda::bowtie2=2.4.2 -> perl
bioconda::meme=5.1.1 -> perl[version='>=5.26.2,<5.26.3.0a0']

Package wheel conflicts for:
conda-forge::python=3.7.3 -> pip -> wheel
bioconda::rseqc=4.0.0 -> pip -> wheel

Package numexpr conflicts for:
bioconda::umi_tools=1.1.1 -> pandas[version='>=0.12.0'] -> numexpr[version='>=2.6.8|>=2.7.0|>=2.7.1|>=2.7.3']
bioconda::icount=2.0.0 -> pandas -> numexpr[version='>=2.6.8|>=2.7.0|>=2.7.1|>=2.7.3']

Package openblas conflicts for:
bioconda::piranha=1.2.1 -> gsl[version='>=2.4,<2.5.0a0'] -> openblas[version='0.2.19|0.2.19.|0.2.20|0.2.20.|>=0.3.3,<0.3.4.0a0']
bioconda::piranha=1.2.1 -> openblas[version='>=0.2.20,<0.2.21.0a0']

Package libiconv conflicts for:
bioconda::meme=5.1.1 -> libxml2[version='>=2.9.10,<2.10.0a0'] -> libiconv[version='>=1.15,<2.0.0a0|>=1.16,<2.0.0a0|>=1.17,<2.0a0|>=1.16,<2.0a0']
bioconda::fastqc=0.11.9 -> fontconfig -> libiconv[version='1.15|>=1.15,<2.0.0a0']

Package xorg-libxrender conflicts for:
bioconda::rseqc=4.0.0 -> r-base -> xorg-libxrender
bioconda::fastqc=0.11.9 -> openjdk[version='>=8.0.144'] -> xorg-libxrender

Package curl conflicts for:
bioconda::icount=2.0.0 -> bedtools[version='>=2.26.0'] -> curl[version='>=7.59.0,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0|>=7.87.0,<8.0a0|>=7.83.1,<8.0a0|>=7.81.0,<8.0a0|>=7.76.0,<8.0a0|>=7.71.1,<8.0a0|>=7.69.1,<8.0a0|>=7.75.0,<8.0a0']
bioconda::pureclip=1.3.1 -> bedtools -> curl[version='>=7.64.1,<8.0a0']
bioconda::rseqc=4.0.0 -> pybigwig -> curl[version='>=7.44.0,<8|>=7.59.0,<8.0a0|>=7.64.1,<8.0a0|>=7.87.0,<8.0a0|>=7.83.1,<8.0a0|>=7.81.0,<8.0a0|>=7.76.0,<8.0a0|>=7.71.1,<8.0a0|>=7.69.1,<8.0a0|>=7.64.0,<8.0a0|>=7.75.0,<8.0a0']

Package future conflicts for:
bioconda::multiqc=1.9 -> future[version='>0.14.0']
bioconda::umi_tools=1.1.1 -> future
bioconda::multiqc=1.9 -> lzstring -> future

Package numpy conflicts for:
bioconda::rseqc=4.0.0 -> numpy
bioconda::rseqc=4.0.0 -> bx-python -> numpy[version='1.10.|1.12.|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.17.5,<2.0a0|>=1.16.5,<2.0a0|>=1.20.0,<2.0a0|>=1.19.1,<2.0a0|>=1.18.5,<2.0a0|>=1.18.4,<2.0a0|>=1.16.4,<2.0a0|>=1.17.0,<2.0a0|>=1.16.3,<2.0a0|>=1.16.2,<2.0a0|>=1.16.1,<2.0a0|>=1.15.4,<2.0a0|>=1.15.2,<2.0a0|>=1.15.1,<2.0a0|1.15.|>=1.9.3,<2.0a0|1.13.']

Package isl conflicts for:
bioconda::preseq=2.0.3 -> libgcc -> isl
bioconda::piranha=1.2.1 -> libgcc -> isl

Package samtools conflicts for:
bioconda::rseqc=4.0.0 -> pysam -> samtools[version='1.3|1.3.1.|1.3.1|1.5.|1.6.|1.7|1.7.|1.9.|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3,<1.4|>=1.3']
bioconda::samtools=1.11
bioconda|bioconda::samtools=1.11
bioconda::icount=2.0.0 -> pybedtools -> samtools[version='1.3|1.3.1.|1.3.1|1.5.|1.6.|1.7|1.7.|1.9.|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3,<1.4|>=1.3']The following specifications were found to be incompatible with your system:

feature:/linux-64::__glibc==2.31=0
feature:|@/linux-64::__glibc==2.31=0
bioconda::bedtools=2.29.2 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
bioconda::bowtie2=2.4.2 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
bioconda::cutadapt=3.0 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
bioconda::meme=5.1.1 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
bioconda::multiqc=1.9 -> click -> __win
bioconda::paraclu=9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
bioconda::piranha=1.2.1 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
bioconda::preseq=2.0.3 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
bioconda::rseqc=4.0.0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
bioconda::samtools=1.11 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
bioconda::subread=2.0.1 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
bioconda::umi_tools=1.1.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
conda-forge::perl=5.26.2 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
conda-forge::python=3.7.3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31 `

this continues solving forever and eventually fails for good. This is the same case if i just try to recreate the conda env for the repo itself and if i follow the docs and first create the nextflow env then add the packages. I would also like to say, I know a container service would be optimal here, but my HPC (U Iowa) does not allow for the usage of such.

change smrna to ncrna for pre-mapping fa

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

option to run icount metagene on peaks

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

MODULE: iCount metagene

MPI error but it should be running locally

I am sorry to be writing 2 out of two bug reports for the pipeline in just a few days, but I seem to be good at breaking things :/

Check Documentation

I have checked the following places for your error:

Description of the bug

I am running the test version of the pipeline, and it the test was successful, as reported in #29, however since a few daysm Friday to be precise, the test is failing with an MPI error. However it shold be running with executor = local which I believe is the default. This error as now occurred in 3 different machines with 2 different versions of Ubuntu (18.04 and 20.04).

Steps to reproduce

Steps to reproduce the behaviour:

Command line: nextflow run nf-core/clipseq -profile test,singularity -r dev
See error:

Pipeline Release  : dev
Run Name          : jovial_gautier
Input             : https://raw.githubusercontent.com/nf-core/clipseq/dev/assets/test_data/reads/prpf8-metadata.csv
Fasta ref         : https://raw.githubusercontent.com/nf-core/clipseq/dev/assets/test_data/fasta/chr20.fa.gz
SmalRNA ref       : [https://raw.githubusercontent.com/nf-core/clipseq/dev/assets/small_rna/Homo_sapiens/Homo_sapiens.final.smallRNA.fa.gz]
Deduplicate       : true
UMI separator     : :
Max Resources     : 6 GB memory, 2 cpus, 2d time per job
Container         : singularity - nfcore/clipseq:dev
Output dir        : test
Launch dir        : /home/domingue/Documents/projects/test_nf
Working dir       : /home/domingue/Documents/projects/test_nf/work
Script dir        : /home/domingue/.nextflow/assets/nf-core/clipseq
User              : domingue
Config Profile    : test,singularity
Config Profile Description: Minimal test dataset to check pipeline function
Config Files      : /home/domingue/.nextflow/assets/nf-core/clipseq/nextflow.config
----------------------------------------------------
[-        ] process > get_software_versions      -
[-        ] process > generate_premap_index      -
[-        ] process > get_software_versions      -
[-        ] process > generate_premap_index      -
[-        ] process > get_software_versions      -
[-        ] process > generate_premap_index      -
executor >  local (8)
[45/374dba] process > get_software_versions                                     [100%] 1 of 1, failed: 1 ✘
[8b/eb308f] process > generate_premap_index (Homo_sapiens.final.smallRNA.fa.gz) [100%] 1 of 1 ✔
[95/787189] process > decompress_fasta (chr20.fa.gz)                            [100%] 1 of 1 ✔
[31/9623d8] process > generate_fai (chr20.fa)                                   [  0%] 0 of 1
[-        ] process > check_genome_size                                         -
[-        ] process > generate_star_index_no_gtf                                -
[8a/9039dc] process > fastqc (exp2)                                             [100%] 2 of 2 ✔
[29/ecca84] process > cutadapt (exp1)                                           [100%] 2 of 2 ✔
[-        ] process > premap                                                    [  0%] 0 of 2
[-        ] process > align                                                     -
[-        ] process > preseq                                                    -
[-        ] process > dedup                                                     -
[-        ] process > get_crosslinks                                            -
[-        ] process > clipqc                                                    -
[-        ] process > multiqc                                                   -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (1)

Command executed:

  echo 1.0.0dev > v_pipeline.txt
  echo 20.10.0 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  cutadapt --version > v_cutadapt.txt
  bowtie2 --version > v_bowtie2.txt
  STAR --version > v_star.txt
  samtools --version > v_samtools.txt
  umi_tools --version > v_umi_tools.txt
  bedtools --version > v_bedtools.txt
  preseq 2> v_preseq.txt
  # subread-align -v 2> v_subread.txt
  bam2fq.py --version > v_rseqc.txt
  iCount --version > v_icount.txt
  pureclip --version > v_pureclip.txt
  Piranha -about 2> v_piranha.txt
  echo "9" > v_paraclu.txt # Paraclu does not output a version
  meme -version > v_meme.txt
  echo $(R --version 2>&1) > v_R.txt
  python --version > v_python.txt
  pygmentize -V > v_pygments.txt
  pigz --version > v_pigz.txt
  perl -v > v_perl.txt
  
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  1

Command output:
  (empty)

Command error:
  --------------------------------------------------------------------------
  A call to mkdir was unable to create the desired directory:
  
    Directory: /ompi.domingue-XPS13-9333.1000
    Error:     Read-only file system
  
  Please check to ensure you have adequate permissions to perform
  the desired operation.
  --------------------------------------------------------------------------
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 107
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 346
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file ess_singleton_module.c at line 340
executor >  local (8)
[45/374dba] process > get_software_versions                                     [100%] 1 of 1, failed: 1 ✘
[8b/eb308f] process > generate_premap_index (Homo_sapiens.final.smallRNA.fa.gz) [100%] 1 of 1 ✔
[95/787189] process > decompress_fasta (chr20.fa.gz)                            [100%] 1 of 1 ✔
[31/9623d8] process > generate_fai (chr20.fa)                                   [  0%] 0 of 1
[-        ] process > check_genome_size                                         -
[-        ] process > generate_star_index_no_gtf                                -
[8a/9039dc] process > fastqc (exp2)                                             [100%] 2 of 2 ✔
[29/ecca84] process > cutadapt (exp1)                                           [100%] 2 of 2 ✔
[-        ] process > premap                                                    [  0%] 0 of 2
[-        ] process > align                                                     -
[-        ] process > preseq                                                    -
[-        ] process > dedup                                                     -
[-        ] process > get_crosslinks                                            -
[-        ] process > clipqc                                                    [  0%] 0 of 1
[-        ] process > multiqc                                                   -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (1)

Command executed:

  echo 1.0.0dev > v_pipeline.txt
  echo 20.10.0 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  cutadapt --version > v_cutadapt.txt
  bowtie2 --version > v_bowtie2.txt
  STAR --version > v_star.txt
  samtools --version > v_samtools.txt
  umi_tools --version > v_umi_tools.txt
  bedtools --version > v_bedtools.txt
  preseq 2> v_preseq.txt
  # subread-align -v 2> v_subread.txt
  bam2fq.py --version > v_rseqc.txt
  iCount --version > v_icount.txt
  pureclip --version > v_pureclip.txt
  Piranha -about 2> v_piranha.txt
  echo "9" > v_paraclu.txt # Paraclu does not output a version
  meme -version > v_meme.txt
  echo $(R --version 2>&1) > v_R.txt
  python --version > v_python.txt
  pygmentize -V > v_pygments.txt
  pigz --version > v_pigz.txt
  perl -v > v_perl.txt
  
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  1

Command output:
  (empty)

Command error:
  --------------------------------------------------------------------------
  A call to mkdir was unable to create the desired directory:
  
    Directory: /ompi.domingue-XPS13-9333.1000
    Error:     Read-only file system
  
  Please check to ensure you have adequate permissions to perform
  the desired operation.
  --------------------------------------------------------------------------
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 107
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 346
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file ess_singleton_module.c at line 340
executor >  local (8)
[45/374dba] process > get_software_versions                                     [100%] 1 of 1, failed: 1 ✘
[8b/eb308f] process > generate_premap_index (Homo_sapiens.final.smallRNA.fa.gz) [100%] 1 of 1 ✔
[95/787189] process > decompress_fasta (chr20.fa.gz)                            [100%] 1 of 1 ✔
[31/9623d8] process > generate_fai (chr20.fa)                                   [100%] 1 of 1 ✔
[-        ] process > check_genome_size                                         -
[-        ] process > generate_star_index_no_gtf                                -
[8a/9039dc] process > fastqc (exp2)                                             [100%] 2 of 2 ✔
[29/ecca84] process > cutadapt (exp1)                                           [100%] 2 of 2 ✔
[-        ] process > premap                                                    [  0%] 0 of 2
[-        ] process > align                                                     -
[-        ] process > preseq                                                    -
[-        ] process > dedup                                                     -
[-        ] process > get_crosslinks                                            -
[-        ] process > clipqc                                                    [  0%] 0 of 1
[-        ] process > multiqc                                                   -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (1)

Command executed:

  echo 1.0.0dev > v_pipeline.txt
  echo 20.10.0 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  cutadapt --version > v_cutadapt.txt
  bowtie2 --version > v_bowtie2.txt
  STAR --version > v_star.txt
  samtools --version > v_samtools.txt
  umi_tools --version > v_umi_tools.txt
  bedtools --version > v_bedtools.txt
  preseq 2> v_preseq.txt
  # subread-align -v 2> v_subread.txt
  bam2fq.py --version > v_rseqc.txt
  iCount --version > v_icount.txt
  pureclip --version > v_pureclip.txt
  Piranha -about 2> v_piranha.txt
  echo "9" > v_paraclu.txt # Paraclu does not output a version
  meme -version > v_meme.txt
  echo $(R --version 2>&1) > v_R.txt
  python --version > v_python.txt
  pygmentize -V > v_pygments.txt
  pigz --version > v_pigz.txt
  perl -v > v_perl.txt
  
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  1

Command output:
  (empty)

Command error:
  --------------------------------------------------------------------------
  A call to mkdir was unable to create the desired directory:
  
    Directory: /ompi.domingue-XPS13-9333.1000
    Error:     Read-only file system
  
  Please check to ensure you have adequate permissions to perform
  the desired operation.
  --------------------------------------------------------------------------
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 107
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 346
  [domingue-XPS13-9333:06359] [[0,1],0] ORTE_ERROR_LOG: Error in file ess_singleton_module.c at line 340
  --------------------------------------------------------------------------
  It looks like orte_init failed for some reason; your parallel process is
  likely to abort.  There are many reasons that a parallel process can
  fail during orte_init; some of which are due to configuration or
  environment problems.  This failure appears to be an internal failure;
  here's some additional information (which may only be relevant to an
  Open MPI developer):
  
    orte_session_dir failed
    --> Returned value Error (-1) instead of ORTE_SUCCESS
  --------------------------------------------------------------------------
  --------------------------------------------------------------------------
  It looks like orte_init failed for some reason; your parallel process is
  likely to abort.  There are many reasons that a parallel process can
  fail during orte_init; some of which are due to configuration or
  environment problems.  This failure appears to be an internal failure;
  here's some additional information (which may only be relevant to an
  Open MPI developer):
  
    orte_ess_init failed
    --> Returned value Error (-1) instead of ORTE_SUCCESS
  --------------------------------------------------------------------------
  --------------------------------------------------------------------------
  It looks like MPI_INIT failed for some reason; your parallel process is
  likely to abort.  There are many reasons that a parallel process can
  fail during MPI_INIT; some of which are due to configuration or environment
  problems.  This failure appears to be an internal failure; here's some
  additional information (which may only be relevant to an Open MPI
  developer):
  
    ompi_mpi_init: ompi_rte_init failed
    --> Returned "Error" (-1) instead of "Success" (0)
  --------------------------------------------------------------------------
  *** An error occurred in MPI_Init
  *** on a NULL communicator
  *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
  ***    and potentially your MPI job)
  [domingue-XPS13-9333:06359] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!

Work dir:
  /home/domingue/Documents/projects/test_nf/work/45/374dbac7549d3892defd6eb734cd9d

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Expected behaviour

The test should pass without errors and results generated.

Log files

Have you provided the following extra information/files:

The command used to run the pipeline
The .nextflow.log file - see next message

System

Hardware: Desktop, VM in a server
Executor:local
OS: Linux Ubuntu
Version 18.04 d 20.04

Nextflow Installation

Version: nextflow version 20.10.0.5430

Container engine

Engine: Singularity
version: singularity version 3.5.2
Image tag: nfcore/clipseq dev

Additional context

The pipeline does not stop by itself, only with ctrl+c

Reads with / characters in the read names cause the pipeline to fail

Check Documentation

I have checked the following places for your error:

Description of the bug

If / characters are in the read names, then the pipeline will fail at the dedup step. This is caused, however, by STAR truncating read names based on the / character. This removes the UMI information which was added earlier in the pipeline, causing the dedup step to fail.

Steps to reproduce

Steps to reproduce the behaviour:

Running the pipeline with reads with a / in the read name. Example

Expected behaviour

Either a verbose error message saying that the reads are incompatible, or automatic removal or replacement of the / characters.

demultiplexing

group analysis

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

make conda test pass for peka module

Check Documentation

I have checked the following places for your error:

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

Command line:
See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

The command used to run the pipeline
The .nextflow.log file

System

Hardware:
Executor:
OS:
Version

Nextflow Installation

Version:

Container engine

Engine:
version:
Image tag:

Additional context

STAR binary on the container does not work with singularity

Check Documentation

I have checked the following places for your error:

Description of the bug

The current container has old software version that are incompatible to modern linux kernels. It works fine with docker, but it's not working with singularity. The problem is specific with STAR:

file STAR
> STAR: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, for GNU/Linux 2.6.18, with debug_info, not stripped

This release is from 2006. Is it possible to provide a more recent container for the workflow?

Steps to reproduce

Steps to reproduce the behaviour:

Command line:

# clean pull
rm -rf  ~/.nextflow/assets/nf-core/clipseq/
# Checking nf-core/clipseq ...
# downloaded from https://github.com/nf-core/clipseq.git - revision: a8653ee5c7 [master]
nextflow run nf-core/clipseq -profile test,singularity

See error:

N E X T F L O W  ~  version 22.10.7
Launching `https://github.com/nf-core/clipseq` [serene_gutenberg] DSL1 - revision: a8653ee5c7 [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/clipseq **v1.0.0**

[16/88cda4] NOTE: Process `get_software_versions` terminated with an error exit status (139) -- Execution is retried (1)
[ab/e7b9b4] NOTE: Process `generate_star_index_no_gtf (chr20.fa)` terminated with an error exit status (139) -- Execution is retried (1)
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (139)

Command executed:

  echo 1.0.0 > v_pipeline.txt
  echo 22.10.7 > v_nextflow.txt
  fastqc --version > v_fastqc.txt
  multiqc --version > v_multiqc.txt
  cutadapt --version > v_cutadapt.txt
  bowtie2 --version > v_bowtie2.txt
  STAR --version > v_star.txt
  samtools --version > v_samtools.txt
  umi_tools --version > v_umi_tools.txt
  bedtools --version > v_bedtools.txt
  preseq 2> v_preseq.txt
  # subread-align -v 2> v_subread.txt
  bam2fq.py --version > v_rseqc.txt
  iCount --version > v_icount.txt
  pureclip --version > v_pureclip.txt
  Piranha -about 2> v_piranha.txt
  echo "9" > v_paraclu.txt # Paraclu does not output a version
  meme -version > v_meme.txt
  python --version > v_python.txt
  pygmentize -V > v_pygments.txt
  pigz --version 2> v_pigz.txt
  perl -v > v_perl.txt

  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  139

Command output:
  (empty)

Command error:
  .command.sh: line 8: 2817176 Segmentation fault      STAR --version > v_star.txt

Work dir:
  $HOME/work/e2/6c1cd23d2002f2040d18756102abe3

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Expected behaviour

I expected the test to work without issues.

Log files

Have you provided the following extra information/files:

The command used to run the pipeline
The .nextflow.log file

System

Hardware: HPC
Executor: local and slurm
OS: debian
Version Debian GNU/Linux 11 (bullseye)

Nextflow Installation

Version: 22.10.7

Container engine

Engine: singularity
version: 3.8.7
Image tag: nfcore/clipseq:1.0.0

Additional context

(1).nextflow.log

Process `get_software_versions` terminated with an error exit status （1）

#command and err

Command line: nextflow run nf-core/clipseq -profile conda
--input /home/gl/nfclip/bp.txt
--fasta /mnt/d/f/X101SC21113826-Z01-F001/Genomes/genome.fa.gz
--genome mm10
--max_memory '6.GB'

2.error:Error executing process > 'get_software_versions'

Caused by:
Process get_software_versions terminated with an error exit status (1)

Command executed:

echo 1.0.0 > v_pipeline.txt
echo 22.10.1 > v_nextflow.txt
fastqc --version > v_fastqc.txt
multiqc --version > v_multiqc.txt
cutadapt --version > v_cutadapt.txt
bowtie2 --version > v_bowtie2.txt
STAR --version > v_star.txt
samtools --version > v_samtools.txt
umi_tools --version > v_umi_tools.txt
bedtools --version > v_bedtools.txt
preseq 2> v_preseq.txt
subread-align -v 2> v_subread.txt
executor > local (2)
[db/361bc7] process > get_software_versions [100%] 1 of 1, failed:1✘
[19/7c4198] process > generate_premap_index (Mus_musculus.smallRNA.fa.gz) [100%] 1 of 1, cached:1✔
[92/12947a] process > decompress_fasta (genome.fa.gz) [100%] 1 of 1, cached:1✔
[- ] process > generate_fai [ 0%] 0 of 1
[81/f04847] process > fastqc (BP_input_1) [100%] 4 of 4, cached: 4 ✔
[8c/e9761e] process > cutadapt (BP_input_2) [100%] 4 of 4, cached: 4 ✔
[- ] process > premap [ 0%] 0 of 4
[- ] process > align -
[- ] process > preseq -
[- ] process > dedup -
[- ] process > rseqc -
[- ] process > get_crosslinks -
[- ] process > clipqc -
[- ] process > multiqc -
[46/85cdc1] process > output_documentation [ 0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'

Caused by:
Process get_software_versions terminated with an error exit status (1)

Command executed:

scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
1

Command output:
pigz 2.6

Command error:
pigz 2.6

Work dir:
/home/gl/work/db/361bc7d9ad5b1f200ce141bc565c50

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

Genome reference gtf not found: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf

Expected behaviour

work/db/361bc7d9ad5b1f200ce141bc565c50/ v_pigz.txt=null It should be printed pigz 2.6 as Command error mentioned, but it was null. And rest of these version-files are all printed correctly.

Log files

scrape_software_versions.py &> software_versions_mqc.yaml

System

WSL2
ubuntu 22.04

Nextflow Installation

N E X T F L O W
version 22.10.1 build 5828
created 27-10-2022 16:58 UTC (28-10-2022 00:58 CDT)
cite doi:10.1038/nbt.3820
http://nextflow.io

Version:

Container engine

Engine: conda
version: conda 22.9.0
Image tag: nf-core/clipseq v1.0.0

Additional context

I've tried many methods about error exit status 1 and that don't work. Is it a written permisson issue? Thx so much~

CLIPSEQ: Migrate all usage parameters for JSON Schema

Hi!

this is not necessarily an issue with the pipeline, but in order to streamline the documentation group next week for the hackathon, I'm opening issues in all repositories / pipeline repos that might need this update to switch from parameter docs to auto-generated documentation based on the JSON schema.

This will then supersede any further parameter documentation, thus making things a bit easier :-)

If this doesn't apply (anymore), please close the issue. Otherwise, I'm hoping to have some helping hands on this next week in the documentation team on Slack https://nfcore.slack.com/archives/C01QPMKBYNR

BAM entry point

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

MODULE: peka

documentation for 2.0

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

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nf-core / clipseq Goto Github PK

clipseq's Introduction

Introduction

Pipeline Summary

Quick Start

Documentation

Credits

Contributions and Support

Citations

clipseq's People

Contributors

Stargazers

Watchers

Forkers

clipseq's Issues

Check Documentation

Description of the bug

Steps to reproduce

Expected behaviour

Log files

System

Nextflow Installation

Container engine

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Check Documentation

Description of the bug

Log files

System

Nextflow Installation

Container engine

Check Documentation

Description of the bug

Steps to reproduce

Expected behaviour

Log files

System

Nextflow Installation

Container engine

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Additional context

Check Documentation

Description of the bug

Steps to reproduce

Expected behaviour

Log files

System

Nextflow Installation

Container engine

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Check Documentation

Description of the bug

Steps to reproduce

Expected behaviour

Log files

System

Nextflow Installation

Container engine

Additional context

Check Documentation

Description of the bug

Steps to reproduce

Expected behaviour

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context