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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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An error that occurred at Step 18. #377

Closed Rui-Jing closed 2 years ago

Rui-Jing commented 3 years ago

Hi, Recently , I used Infercnv to process my single-cell data. In the STEP 18, an error occurred.

Error is: STEP 18: Run Bayesian Network Model on HMM predicted CNV's

INFO [2021-11-16 05:01:28] Creating the following Directory: /home/pc/infercnv//BayesNetOutput.HMMi6.rand_trees.hmm_mode-subclusters INFO [2021-11-16 05:01:28] Initializing new MCM InferCNV Object. INFO [2021-11-16 05:01:28] validating infercnv_obj Error in (function (cl, name, valueClass) : assignment of an object of class “character” is not valid for @‘cnv_regions’ in an object of class “MCMC_inferCNV”; is(value, "factor") is not TRUE

My code

infercnv_obj = CreateInfercnvObject( raw_counts_matrix=counts_p121_2, annotations_file="/home/pc/p121_2_annotation.txt", delim="\t", gene_order_file="/home/zfzf/mm_geneOrderingFile.txt", ref_group_names=c("P121_2_Oligodendrocytes","P121_2_Macrophages","P121_2_Microglia-1", "P121_2_Proliferation-related immune cells","P121_2_Microglia-2","P121_2_Ependymal cells"))

infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1, out_dir="/home/pc/infercnv/", cluster_by_groups=FALSE, analysis_mode="subclusters", denoise=TRUE, HMM=TRUE, HMM_type = "i6", num_threads=4)

My infercnv version is 1.3.3 I sincerely hope to get your kind help.

GeorgescuC commented 3 years ago

Hi @Rui-Jing ,

Version 1.3.3 is very outdated at this point, and it's likely the issue is fixed in the current version of infercnv. After an update, you may want to delete the current output folder for the reload not to mistakenly reload the old object that will probably produce errors.

Regards, Christophe.

Joya-zy commented 1 year ago

Hi @Rui-Jing ,

Version 1.3.3 is very outdated at this point, and it's likely the issue is fixed in the current version of infercnv. After an update, you may want to delete the current output folder for the reload not to mistakenly reload the old object that will probably produce errors.

Regards, Christophe.

Hi~ @GeorgescuC I downloaded version 1.3.3 infercnv installation package from the website https://github.com/broadinstitute/infercnv/releases, which showed the date of update is Feb 8, 2020. However, I still met the same problem at run time, is this the latest version? Looking forward to your kindly reply~ Thanks!