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gjeunen / reference_database_creator

creating reference databases for amplicon sequencing
MIT License
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OverflowError #57

Closed LuciaRanieri97 closed 1 month ago

LuciaRanieri97 commented 7 months ago

Hi everyone, today, after a pcr in silico command I have got this error. Can you help me?

ERROR: Traceback (most recent call last): File "/home/utente/anaconda2/envs/CRABS/lib/python3.6/site-packages/cutadapt/pipeline.py", line 574, in run for chunk_index, chunk in enumerate(dnaio.read_chunks(f, self.buffer_size)): File "/home/utente/anaconda2/envs/CRABS/lib/python3.6/site-packages/dnaio/chunks.py", line 80, in read_chunks raise OverflowError: FASTA/FASTQ record does not fit into buffer

Thanks in advance!!! :)

gjeunen commented 7 months ago

Hello @LuciaRanieri97,

The error points to a sequence being too long for cutadapt to handle, which CRABS uses during the in silico PCR analysis. This probably occurred by downloading full genome sequences. The recommendation is to avoid longer fragments than mitochondrial and chloroplast genomes. Would this be a suitable option for your use-case or are the genomes essential to be incorporated in the database?

Best regards, Gert-Jan

LuciaRanieri97 commented 7 months ago

Thank you very much for the timely response. I can proceed by streamlining the initial database!

Best regards, Lucia