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PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
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Unable to run my PacBio data with snakemake and pbassembly #713

Closed wjj666 closed 3 years ago

wjj666 commented 3 years ago

I convert sequel bams to fasta (using bam2fasta) and use them as input for falcon. But I got an error like this:

ValueError: Error tokenizing FASTA header

Referring to this issue, I tried the snakemake workflow, but there was another error:

File "/XXX/Anaconda3/envs/falcon/lib/python3.7/site-packages/falcon_kit/io.py", line 147, in deserialize raise Exception('Unknown extension for {!r}'.format(fn)) Exception: Unknown extension for '../../fc_run.cfg'

The snakemake cmd I used was:

snakemake --config input_fofn=input.fofn config_fn=fc_run.cfg MAKEDIR=/tmp/local/csjjwang/data/NA12878/1_asm/pacbiofalcon --cores 64 -s falcon.clr.snakemake --verbose -p

Could you please help solve these problems and help me assembly my pacbio data with falcon?

Thank you very much.

pb-cdunn commented 3 years ago

Same as #695 and https://github.com/PacificBiosciences/pbbioconda/issues/400