search

canceromics / MeRIPseqPipe

MeRIPseqPipe：An integrated analysis pipeline for MeRIP-seq data based on Nextflow.
MIT License
31 stars 18 forks source link

DSL error DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier #19

Open mathavanpu opened 7 months ago

mathavanpu commented 7 months ago

Hi I am trying to run this pipeline but I got an error as shown below, How to resolve this error
run MeRIPseqPipe-1.0.1/ -profile test,docker N E X T F L O W ~ version 23.10.0 Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier

mathavanpu commented 7 months ago

I am also trying to instal the pipeline using docker

sudo docker pull kingzhuky/meripseqpipe [sudo] password for lifecell: Using default tag: latest Error response from daemon: manifest for kingzhuky/meripseqpipe:latest not found: manifest unknown: manifest unknown

likelet commented 7 months ago

@juneb4869 plz check the error

mathavanpu commented 4 months ago

Hi Could you please check this error @juneb4869

mathavanpu commented 4 months ago

Hi I am trying to execute the test run but I got an error

nextflow run ../MeRIPseqPipe/ -profile test,docker Nextflow 23.10.1 is available - Please consider updating your version to it N E X T F L O W ~ version 23.10.0 Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier

juneb4869 commented 4 months ago

Hi mathavanpu! Can you try to install Nextflow v20.10.0, it works well. To install this pipe using docker: docker pull kingzhuky/meripseqpipe:dev

mathavanpu commented 4 months ago

Hi thank you for your response! Now I can run this script but I got an error in star alignment step

Error executing process > 'StarAlign (WT1_Trimmed)'

Caused by: Process StarAlign (WT1_Trimmed) terminated with an error exit status (102)

Command executed:

STAR --runThreadN 1 --readFilesCommand zcat --twopassMode Basic --genomeDir GRCh38_STAR --readFilesIn WT1_Trimmed_1_aligners.fastq.gz WT1_Trimmed_2_aligners.fastq.gz --outSAMtype BAM Unsorted --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 20 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix WT1_Trimmed > WT1_Trimmed_log.txt

mv WT1_TrimmedAligned.out.bam WT1_Trimmed_star.bam

Command exit status: 102

Command output: (empty)

Command error:

EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "genomeType" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

May 19 17:19:45 ...... FATAL ERROR, exiting

Work dir: /goast/Work/RRBS/Trial/MeRIPseqPipe/work/74/47b4f366e799928d21af0aa611d053

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

ESC[0;35m[MeRIPseqPpipe]ESC[0;31m Pipeline completed with errorsESC[0m WARN: Killing running tasks (2) WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info. (END) error.log

juneb4869 commented 4 months ago

It seems to be an error in the STAR index. For example, the correct index would be: --star_index /data1/public/Database/human/hg38/starindex image Please check you files in --genomeDir GRCh38_STAR

mathavanpu commented 4 months ago

Hi I am guessing this error may be due to the STAR aligner version. How can I use a specific version?

juneb4869 commented 4 months ago

Hi! You can try to set the param: -profile local,docker，or don't specify the param:--star_index.

mathavanpu commented 4 months ago

Hi Thank you very much for your prompt response Your support is greatly appreciated!!!

I got an error mentioned below, command used NXF_VER=22.10.0 nextflow main.nf -c nextflow.config -bg -profile docker --designfile ../designfile.tsv --comparefile ../compare.txt --aligners star --fasta /Academic/GenomeReference/HomoSapiens_GRCh38.p13/GRCh38.p13.genome.fa --gtf /Academic/GenomeReference/HomoSapiens_GRCh38.p13/gencode.v40.basic.annotation.gtf --outdir Meripout --skip_createbedgraph --peakMerged_mode rank --skip_meyer --skip_matk --methylation_analysis_mode Wilcox-test -resume

Error Message mkdir StarIndex STAR --runThreadN 20 --runMode genomeGenerate --genomeDir StarIndex --genomeFastaFiles GRCh38.p13.genome.fa --sjdbGTFfile gencode.v40.basic.annotation.gtf --sjdbOverhang 49 --limitGenomeGenerateRAM 36000000000

Command exit status: 104

Command output: May 21 15:43:09 ..... started STAR run May 21 15:43:09 ... starting to generate Genome files May 21 15:44:23 ... starting to sort Suffix Array. This may take a long time... May 21 15:45:02 ... sorting Suffix Array chunks and saving them to disk... May 21 16:10:08 ... loading chunks from disk, packing SA... May 21 16:12:25 ... finished generating suffix array May 21 16:12:25 ... generating Suffix Array index May 21 16:16:24 ... completed Suffix Array index May 21 16:16:24 ..... processing annotations GTF

Command error: May 21 15:43:09 ..... started STAR run May 21 15:43:09 ... starting to generate Genome files May 21 15:44:23 ... starting to sort Suffix Array. This may take a long time... May 21 15:45:02 ... sorting Suffix Array chunks and saving them to disk... May 21 16:10:08 ... loading chunks from disk, packing SA... May 21 16:12:25 ... finished generating suffix array May 21 16:12:25 ... generating Suffix Array index May 21 16:16:24 ... completed Suffix Array index May 21 16:16:24 ..... processing annotations GTF

Fatal INPUT FILE error, no valid exon lines in the GTF file: gencode.v40.basic.annotation.gtf Solution: check the formatting of the GTF file. Most likely cause is the difference in chromosome naming between GTF and FASTA file.

May 21 16:16:36 ...... FATAL ERROR, exiting

Work dir: /goast/Work/RRBS/Trial/MeRIPseqPipe/work/83/f1777fb4b14cdde97f58ca97f5c36d

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

Execution cancelled -- Finishing pending tasks before exit

also please tell me how to use this --genome (using iGenomes)

juneb4869 commented 4 months ago

GRCh38.p13.genome.fa from Ensembl，it uses '1,2,3' as chr name, but gencode.v40.basic.annotation.gtf uses 'chr1,chr2,chr3' as chr name, plz check the chr name. And you can download the gtf file from Ensembl.

juneb4869 commented 4 months ago

You can try to download fasta file from https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/, and gtf from Gencode.

mathavanpu commented 4 months ago

Hi Thank you very much for your response, I want to change the thread number in the alignment step (STAR), can I use this file nextflow.config. could you please give some examples

juneb4869 commented 4 months ago

Yes! you can edit the number in nextflow.config " max_memory = 128.GB max_cpus = 16 max_time = 240.h "

mathavanpu commented 4 months ago

Hi The MeripSeqPipe completed the QC, rseqc, and alignment steps. For the peak calling step, only two files were completed within two hours, and no other files were processed even after 48 hours(total 12 files). In the background, some processes are still running (191088 mathavan 20 0 88.0g 1.0g 14556 S 0.0 0.1 7:39.59 java). I am not getting any error message For your reference, I have attached the error.log file. Kindly check help me how to resolve this issue.

folder structure ../results_44/ |-- alignment | |-- rRNA_dup | |-- samtoolsSort | -- star |-- peakCalling |-- metpeak | |-- metpeak_J | -- metpeak_L |-- pipeline_info -- QC |-- fastqc -- rseqc |-- bam_stat |-- infer_experiment |-- inner_distance | |-- data | |-- plots |-- rscripts |-- junction_annotation | |-- data | |-- events | |-- junctions | -- rscripts |-- junction_saturation |-- rscripts |-- read_distribution -- read_duplication |-- dup_pos |-- dup_seq -- scripts

[script_error.log](https://github.com/canceromics/MeRIPseqPipe/files/15463535/script_error.log