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Error in Hypomethylated region analysis #12

Open scintilla9 opened 10 months ago

scintilla9 commented 10 months ago

Hi,

Thanks for the methylation analysis pipeline.

I was testing a human WGBS data with msPIPE, and I used UCSC hg38 for reference. When running with run_MethylSeekR.pl, I got the following error message with all chromosome:

[GMA] UMRs and LMRs analysis /msPIPE/bin/GMA/run_MethylSeekR.pl /mnt/NFS/EC2480U-P/cwl/msPIPE/output/Analysis/G1/union_CpG/params.txt /mnt/NFS/EC2480U-P/cwl/msPIPE/output/Analysis/G1/MethylSeekR Loading required package: BSgenome.Hsapiens.UCSC.hg38 File: /mnt/NFS/EC2480U-P/cwl/msPIPE/output/Analysis/G1/union_CpG/chr1.txt chromosome: chr1 output directory: /mnt/NFS/EC2480U-P/cwl/msPIPE/output/Analysis/G1/MethylSeekR reading methylome data Read 1152183 records Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE Calls: ucscTableQuery ... .get_chrom_info_for_registered_UCSC_genome -> GET_CHROM_SIZES -> .order_seqlevels -> stopifnot In addition: Warning message: In .local(x, ...) : 'track' parameter is deprecated now you go by the 'table' instead Use ucscTables(genome, track) to retrieve the list of tables for a track Execution halted

Since there's no output information about UMRs/LMRs in MethylSeekR folder, it cannot generate Circos plot for both experiment groups.

It seems that something to do with GenomeInfoDb or BiocManager.

Could you kindly help me with this issue?

mia110214 commented 9 months ago

Hello, thank you for your interest in msPIPE. Have you tried running the hg38 reference fasta file directly? If so, I recommend trying to execute it by specifying only the assembly version in the options. Additionally, to better understand and assist you, please provide the command you used for execution and the params.txt file.

scintilla9 commented 9 months ago

Hi, Thanks for replay, and sorry for the ambiguous description.

The command I used for msPIPE: docker run --rm -v /mnt:/mnt -v /mnt/NFS/EC2480U-P/cwl/msPIPE/reference:/msPIPE/reference jkimlab/mspipe:latest msPIPE.py -p /mnt/NFS/EC2480U-P/cwl/msPIPE/mspipe.conf -c 40 -q 0.05 -o /mnt/NFS/EC2480U-P/cwl/msPIPE/output/

And I ran msPIPE by supplying reference genome version in config file, like:

[DMR] ANALYSIS1 = G1, G2

[REFERENCE] UCSC_NAME = hg38

[LIB1] SAMPLE_NAME = G1 LIB_NAME = G1_rep1 LIB_TYPE = P FILE_1 = /mnt/NFS/EC2480U-P/cwl/methylseq/TEST23024/rawData/NA12878-1_22GVMNLT3_L1_R1.fastq.gz FILE_2 = /mnt/NFS/EC2480U-P/cwl/methylseq/TEST23024/rawData/NA12878-1_22GVMNLT3_L1_R2.fastq.gz

[LIB2] SAMPLE_NAME = G2 LIB_NAME = G2_rep1 LIB_TYPE = P FILE_1 = /mnt/NFS/EC2480U-P/cwl/methylseq/TEST23024/rawData/NA12878-cfDNA-1_22GVMNLT3_L1_R1.fastq.gz FILE_2 = /mnt/NFS/EC2480U-P/cwl/methylseq/TEST23024/rawData/NA12878-cfDNA-1_22GVMNLT3_L1_R2.fastq.gz ...

The params.txt file for visualization is attached: params.txt

Thanks for your help!