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I am running cnvkit.py import-rna, and it gave me the following error: the cnvkit version is 0.9.9.
(cnvkit) limin@DERM-6NBQ05N-LT cnr % cnvkit.py import-rna -f counts -g /Users/limin/miniconda3/envs/cnvkit/data/ensembl-gene-info.hg38.tsv -c /Users/limin/miniconda3/envs/cnvkit/data/tcga-skcm.cnv-expr-corr.tsv -o output.txt ../txt/*.txt Dropping 16105 / 18085 rarely expressed genes from input samples Loading gene metadata and TCGA gene expression/CNV profiles Loaded /Users/limin/miniconda3/envs/cnvkit/data/ensembl-gene-info.hg38.tsv with shape: (221323, 9) Loaded /Users/limin/miniconda3/envs/cnvkit/data/tcga-skcm.cnv-expr-corr.tsv with shape: (19177, 4) Resetting 2846 ambiguous genes' correlation coefficients to default 0.100000 Trimmed gene info table to shape: (63966, 13) Aligning gene info to sample gene counts Weighting genes with below-average read counts Calculating normalized gene read depths /Users/limin/miniconda3/envs/cnvkit/lib/python3.7/site-packages/numpy/lib/function_base.py:4009: RuntimeWarning: invalid value encountered in subtract diff_b_a = subtract(b, a) Weighting genes by spread of read depths Weighting genes by spearman_r correlation coefficient Weighting genes by pearson_r correlation coefficient Weighting genes by kendall_t correlation coefficient /Users/limin/miniconda3/envs/cnvkit/lib/python3.7/site-packages/scipy/stats/stats.py:283: RuntimeWarning: divide by zero encountered in log log_a = np.log(a) Writing output files Wrote output.txt with 1980 rows Traceback (most recent call last): File "/Users/limin/miniconda3/envs/cnvkit/bin/cnvkit.py", line 9, in <module> args.func(args) File "/Users/limin/miniconda3/envs/cnvkit/lib/python3.7/site-packages/cnvlib/commands.py", line 1555, in _cmd_import_rna for cnr in cnrs: File "/Users/limin/miniconda3/envs/cnvkit/lib/python3.7/site-packages/cnvlib/import_rna.py", line 47, in <genexpr> cnrs = (rna.correct_cnr(cnr, do_gc, do_txlen, max_log2) for cnr in cnrs) File "/Users/limin/miniconda3/envs/cnvkit/lib/python3.7/site-packages/cnvlib/rna.py", line 381, in attach_gene_info_to_cnr assert not gene_minima.hasnans, gene_minima.head() AssertionError: gene_id ENSG00000188157 -5.0 ENSG00000078808 -5.0 ENSG00000160087 -5.0 ENSG00000131584 -5.0 ENSG00000127054 -5.0 dtype: float64
Any suggestions will be very helpful. Thanks.
The text was updated successfully, but these errors were encountered:
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I am running cnvkit.py import-rna, and it gave me the following error:
the cnvkit version is 0.9.9.
Any suggestions will be very helpful. Thanks.
The text was updated successfully, but these errors were encountered: