gravatar for d.w.karjosukarso

2 hours ago by

Hi,
I would like to do CNV analysis on bulk RNA-seq data from cancer cell lines. I made the correlation file
I used the following code:

/home/karjosukarso/anaconda3/envs/CNV/bin/cnvkit.py import-rna -f counts -g /home/karjosukarso/CNVkit/ensembl-gene-info.hg38.tsv -c /home/karjosukarso/DK-53/CNV/tcga-hnsc.cnv-expr-corr.tsv -o output.txt *.txt

But, I got the following error:

Dropping 369445 / 369445 rarely expressed genes from input samples
Loading gene metadata and TCGA gene expression/CNV profiles
Loaded /home/karjosukarso/CNVkit/ensembl-gene-info.hg38.tsv with shape: (221323, 9)
Loaded /home/karjosukarso/DK-53/CNV/tcga-hnsc.cnv-expr-corr.tsv with shape: (20309, 4)
Resetting 2844 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
/home/karjosukarso/anaconda3/envs/CNV/lib/python2.7/site-packages/cnvlib/rna.py:269: FutureWarning: clip_upper(threshold) is deprecated, use clip(upper=threshold) instead
  weights = [np.sqrt((gene_counts / gene_counts.quantile(.75)).clip_upper(1))]
Calculating normalized gene read depths
Traceback (most recent call last):
  File "/home/karjosukarso/anaconda3/envs/CNV/bin/cnvkit.py", line 13, in <module>
    args.func(args)
  File "/home/karjosukarso/anaconda3/envs/CNV/lib/python2.7/site-packages/cnvlib/commands.py", line 1462, in _cmd_import_rna
    args.normal, args.do_gc, args.do_txlen, args.max_log2)
  File "/home/karjosukarso/anaconda3/envs/CNV/lib/python2.7/site-packages/cnvlib/import_rna.py", line 39, in do_import_rna
    gene_info, sample_counts, tx_lengths, normal_ids)
  File "/home/karjosukarso/anaconda3/envs/CNV/lib/python2.7/site-packages/cnvlib/rna.py", line 274, in align_gene_info_to_samples
    normal_ids)
  File "/home/karjosukarso/anaconda3/envs/CNV/lib/python2.7/site-packages/cnvlib/rna.py", line 310, in normalize_read_depths
    assert sample_depths.values.sum() > 0
AssertionError

Could anyone help me what could have gone wrong?
Thank you.

Greetings,
Dyah



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