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Piezoid / pugz

Truly parallel gzip decompression
MIT License
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Nanopore reads terminate called after throwing an instance of 'gzip_error' what(): Got a context from invalid position Aborted #11

Open hjsbio opened 3 years ago

hjsbio commented 3 years ago

Dear authors,

I used this tools to decompress nanopore reads file in gz format. Using command like this: gunzip -t 8 1.pass.fastq.gz > 1.fq but It throw errors like below: terminate called after throwing an instance of 'gzip_error' what(): Got a context from invalid position Aborted

I found that the output file contain some reads but the command failed to continue. Could you help me to solve it .

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rchikhi commented 3 years ago

Hi, is the .gz file publicly available by any chance?

kerekgya commented 3 months ago

I also experienced the same error while trying to decompress the Uniprot TrEMBL database (uniprot_trembl.fasta.gz). Interestingly, the error always ocurs at a different position in the file, to me this suggests that there is some race condition causing this. Using older versions, the error message is programs/../lib/deflate_decompress.hpp:1100: Assertion 'sync_bitpos == upstream_context.second' failed in 'void DeflateThreadRandomAccess::go(size_t)'. There is even a comment in the code: // FIXME: redecompress from this position (with resolved context this time), so this could explain the error. As far as I can tell though, this would be needed for random access, but I am trying to decompress an entire file, so this sholudn't happen???

rchikhi commented 3 months ago

given that further development of this project is not likely, I'd suggest you give https://github.com/mxmlnkn/rapidgzip a try. But thank you for reporting a detailed bug report!!