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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Examining conflicts takes forever installing cnvkit with conda #772

Open HeejunJang opened 1 year ago

HeejunJang commented 1 year ago

Hello

I tried to install cnvkit using conda.

However, it is currently unfinished on the 3rd day.

Only the process of "Examing conflicts ~~" is being repeated over and over again.

Can I solve this problem by changing my other options?

Please Help

Thank you.

tetedange13 commented 1 year ago

Hi @HeejunJang,

In my experience this is due to conda struggling to find compatible packages within a single channel

  1. What is your conda version (output of conda --version)
  2. What is exact conda command you used ?
  3. Do you have any channels specified in your .condarc config file ? (output of conda config --show channels)
  4. What is your "channel priority" ? (output of conda config --show channel_priority)

To install CNVkit (or any "bioinformatics" package/app), I usually type conda create -n <package> -c conda-forge -c bioconda <package> => Order matters, so this tells conda to first look for dependencies in conda-forge, then in bioconda (then in defaults channel, see conda's help) => So here, please try : conda create -n cnvkit -c conda-forge -c bioconda cnvkit (possibly helpful : https://conda-forge.org/docs/user/tipsandtricks.html#how-to-fix-it)

Hope this helps ! Have a nice day, Felix.

HeejunJang commented 1 year ago

Hello, Here's my information.

  1. conda 22.9.0

  2. conda update --all conda install cnvkit

    • conda-forge
    • bioconda
    • defaults

  4. channel_priority: flexible

I'll try with your suggestion and reply again.

Thank you.

Heejun Jang.

HeejunJang commented 1 year ago

Hello,

I installed with "conda create -n cnvkit -c conda-forge -c bioconda cnvkit"

and did "conda activate cnvkit"

But, Simmilar error occured before I ran cnvkit.py (source version) without conda environment.

/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) WARNING: Most antitarget bins (100.00%, 19237/19237) have low or no coverage; is this amplicon/WGS? /usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/cnary.py:451: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning. return pd.concat(resids) if resids else pd.Series([]) Antitargets are nan x more variable than targets Wrote /work/hjjang/CNV/result/NEO83_S25_L001/NEO83_S25_L001.cnr with 22920 regions Segmenting /work/hjjang/CNV/result/NEO83_S25_L001/NEO83_S25_L001.cnr ... Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes Traceback (most recent call last): File "/usr/bin/anaconda3/envs/cnvkit/bin/cnvkit.py", line 9, in args.func(args) File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/commands.py", line 138, in _cmd_batch pool.submit(batch.batch_run_sample, File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/parallel.py", line 19, in submit return SerialFuture(func(args)) File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/batch.py", line 186, in batch_run_sample segments = segmentation.do_segmentation(cnarr, segment_method, File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 61, in do_segmentation rets = list(pool.map(_ds, ((ca, method, threshold, variants, File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 89, in _ds return _do_segmentation(args) File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 161, in _do_segmentation seg_out = core.call_quiet(rscript_path, File "/usr/bin/anaconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/core.py", line 31, in call_quiet raise RuntimeError("Subprocess command failed:\n$ %s\n\n%s" RuntimeError: Subprocess command failed: $ Rscript --no-restore --no-environ /tmp/tmprmliknp7

b'Loading probe coverages into a data frame\nWarning message:\nIn CNA(cbind(tbl$log2), tbl$chromosome, tbl$start, data.type = "logratio", :\n markers with missing chrom and/or maploc removed\n\nSegmenting the probe data\nError in segment(cna, weights = tbl$weight, alpha = 1e-04) : \n length of weights should be the same as the number of probes\nExecution halted\n'

I confirmed that similar errors occur both when running with conda and without conda.

Thank you.

Heejun Jang