cnvkit icon indicating copy to clipboard operation
cnvkit copied to clipboard

cnvkit import-rna AssertionError: gene_id

Open limin321 opened this issue 3 weeks ago • 0 comments

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.

limin321 avatar Feb 05 '25 05:02 limin321