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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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InferCNV #494

Open krigia opened 1 year ago

krigia commented 1 year ago

Hello,

I am running the inferCNV and I am getting the following error:

Error in infercnv::CreateInfercnvObject(raw_counts_matrix = "/Volumes/Pegasus_R4i/PBMC_3k_single_cell_dataset/filtered_gene_bc_matrices/hg19/merged_object_Kam_Dong_sc_count_matrix.txt", : Please make sure that all the annotated cell names match a sample in your data matrix. Attention to: AAACGCTTCCAGTGCG-1_1,AAAGAACAGCAGGCAT-1_1,AAAGAACCATGGGAAC-1_1,AAAGAACGTGCGTTTA-1_1,AAAGGGCTCGTGCGAC-1_1,AAAGTCCGTTCACGAT-1_1,AAAGTGACATTCTGTT-1_1,AAAGTGATCTTGAACG-1_1,AAATGGAGTATCTCGA-1_1,AAATGGAGTTCTAACG-1_1,AAATGGATCCAGTTCC-1_1,AACAAAGAGGATTTCC-1_1,AACAAAGGTCACGCTG-1_1,AACAAAGGTGTCCTAA-1_1,AACAAGAAGGCCTGCT-1_1,AACACACGTGTGGTCC-1_1,AACAGGGCACTATCCC-1_1,AACCACAGTCAGACGA-1_1,AACCATGTCTTGGAAC-1_1,AACCTGAGTGCCTTTC-1_1,AACCTTTTCAACTACG-1_1,AACCTTTTCCCAAGCG-1_1,AACCTTTTCCGCCTAT-1_1,AACGAAATCACTTTGT-1_1,AACGGGAAGCTTAAGA-1_1,AACGGGAGTCCGTACG-1_1,AACTTCTAGACTCTTG-1_1,AACTTCTGTCGTCATA-1_1,AACTTCTGTCTTCTAT-1_1,AAGAACAAGGTGCTAG-1_1,AAGACTCAGGCCATAG-1_1,AAGCATCCATGATAGA-1_1,AAGCCATCACCTTCCA-1_1,AAGCGAGTCTACTGAG-1_1,AAGCGTTCACCCTAAA-1_1,AAGTCGTGTTGCTCCT-1_1,AAGTGAAAGGAACGCT-1_1,AAGTGAACATACAGAA-1_1,AATCACGGTAATCAAG-1_1,AATCACGGTCCAATCA-1_1,AATGACCGTCAAAGCG-1_1,AATGACCGTGGTAATA-1_1,AATGG

Your help is highly appreciated! Thank you.

............................................. The command line I run is:

infercnv_obj_kemeneva_dog <- infercnv::CreateInfercnvObject(raw_counts_matrix="/Volumes/Pegasus_R4i/PBMC_3k_single_cell_dataset/filtered_gene_bc_matrices/hg19/merged_object_Kam_Dong_sc_count_matrix.txt", annotations_file="/Volumes/Pegasus_R4i/PBMC_3k_single_cell_dataset/filtered_gene_bc_matrices/hg19/merged_object_Kam_Dong_sc_cell_annotations.txt", delim="\t", gene_order_file="/Volumes/Pegasus_R4i/gencode_v27.txt", ref_group_names=c("normal"), max_cells_per_group = NULL, min_max_counts_per_cell = c(100, +Inf), chr_exclude = c("chrX", "chrY", "chrM"))

out_dir = tempfile('/Volumes/Pegasus_R4i/NB-scRNA-seq/Public-available-scRNA-seq-datasets/')

infercnv_obj_kam_dog <- infercnv::run(infercnv_obj_kam_dog, cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics out_dir=out_dir, cluster_by_groups=TRUE, denoise=TRUE, HMM=TRUE)

data(infercnv_obj_kam_dog)

infercnv_obj <- infercnv::apply_median_filtering(infercnv_obj_kam_dog)

infercnv::plot_per_group(infercnv_obj_kam_dog, out_dir=out_dir)

GeorgescuC commented 1 year ago

Hi @krigia ,

The issue seems similar to the one reported in https://github.com/broadinstitute/infercnv/issues/455 . Do the listed cell names match exactly in your annotation file? Does the error still occur if you remove the "-1" in the cell names in both files as seems to work in the issue cited above? Which version of infercnv are you running?

Regards, Christophe.

krigia commented 1 year ago

@GeorgescuC Hi Christophe, I have run the latest version of inferCNV at MacOS Ventura 13.1. I had to update the MacOS environment and install multiple dependencies. I will try your suggestion- hopefully it will work.

Thank you