CNVkit for RNA-seq: log2 in *.cnr file is all zero

[jingyu9603]

I am trying to analyze RNA expression data using CNVkit. Here is the code I used: cnvkit.py import-rna ./SRR8613811.txt --gene-resource ../ensembl-gene-info.hg38.tsv --correlations ~/softwave/cnvkit-0.9.10/data/tcga-skcm.cnv-expr-corr.tsv --output test2-summary.tsv --output-dir test2/ The sample read count file has the following form:

Ensembl_ID SRR8613811
ENSG00000000003 365 ENSG00000000005 8 ENSG00000000419 691 ENSG00000000457 711 ENSG00000000460 602 ENSG00000000938 94 ENSG00000000971 820 ENSG00000001036 566 ENSG00000001084 719 ENSG00000001167 1575 ENSG00000001460 320 ENSG00000001461 2061

The code runs smoothly

Dropping 162 / 25299 rarely expressed genes from input samples Loading gene metadata and TCGA gene expression/CNV profiles Loaded ../ensembl-gene-info.hg38.tsv with shape: (221323, 9) │Loaded /home/yj2/softwave/cnvkit-0.9.10/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 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 /home/yj2/miniconda3/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 test2-summary.tsv with 24951 rows Wrote test2/SRR8613811.cnr with 24951 regions

However, when I checked the *.cnr file, I found that the log2 of all the genes was 0. AS follows:

chromosome start end gene log2 depth gc tx_length weight 1 11869 14409 DDX11L1 0 0.54315 0.575 1657 1 1 14404 29570 WASH7P 0 9.10437 0.5443 1351 1 1 131025 134836 CICP27 0 6.29591 0.5971 3812 1 1 185217 195411 FO538757.1 0 10.952 0.5654 1397 1 1 257864 359681 AP006222.1 0 23.6302 0.3998 5603 1 1 347982 348366 RPL23AP24 0 0.519481 0.5039 385 1 1 365389 522928 AL732372.2 0 148.559 0.4261 902 1 1 450703 451697 OR4F29 0 0.301508 0.4573 995 1 1 491225 493241 AL732372.3 0 2.82486 0.6619 1239 1

I don't know what went wrong. Can someone help me? Thank you very much!