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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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RuntimeWarning: invalid value encountered in log1p can_lp = np.log1p(-np.exp(mt_lps).sum()) #286

Closed billytcl closed 2 years ago

billytcl commented 2 years ago

I'm using guppy v6.1.2 with megalodon v2.5.0. I get this error:

/home/billylau/.conda/envs/megalodon2.5.0/lib/python3.8/site-packages/megalodon/mods.py:1831: RuntimeWarning: invalid value encountered in log1p
  can_lp = np.log1p(-np.exp(mod_lps).sum())

I'm not sure what exactly happened. What can I do to check on this?

The invocation:

DBG 09:41:24 : Command: """/home/billylau/.conda/envs/megalodon2.5.0/bin/megalodon fast5_combined/barcode01 --guppy-server-path /mnt/ix1/Resources/tools/ont-guppy/v6.1.2/bin/guppy_basecall_server --guppy-config dna_r9.4.1_450bps_modbases_5hmc_5mc_cg_sup_prom.cfg --remora-modified-bases dna_r9.4.1_e8 sup 0.0.0 5hmc_5mc CG 0 --outputs basecalls mappings mod_mappings mods per_read_mods --reference /mnt/ix1/Resources/GenomeRef/Homo_sapiens/Ensembl/GRCh38_no_alt/Sequence/WholeGenomeFasta/hs38_naa.fna --devices cuda:all --processes 50 --guppy-concurrent-reads 25 --guppy-timeout 1000 --samtools-executable /mnt/ix1/Resources/tools/samtools/v1.10ubuntu20.04/bin/samtools --write-mods-text --output-directory ./megalodon_v6.1.2_5hmC_5mC/barcode01
marcus1487 commented 2 years ago

This has been fixed with the latest Remora release (v1.1.0).