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!

[l0ka]

I have the same issue.. any news?

[MaHaoran627]

Because you used only 1 sample, but 10 is recommended according to their docs: "The cohort size should be at least 5, preferably at least 10 samples." https://cnvkit.readthedocs.io/en/stable/rna.html

[l0ka]

Yes, I figured it out, thanks!