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dr-joe-wirth / phantasm

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
MIT License
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Failed SSL hello #16

Closed astrodea closed 1 year ago

astrodea commented 1 year ago

Hello,

I have tried to run the knownPhyloMarker process with the latest version of the tool and a large number of genetic markers, however I am receiving a new error during the blasting step: Bio.Application.ApplicationError: Non-zero return code 255 from '/usr/bin/blastp -out /data/finalAnalysis/_temp.blastp -outfmt "6 qseqid sseqid stitle staxid sacc pident length mismatch gaps gapopen evalue bitscore" -query /data/finalAnalysis/_temp.faa -db nr -remote', message 'Error: (302.26) [blastp] SSOCK#59000[5]@130.14.29.110:443: [SOCK::Connect] Failed SSL hello: Timeout[30.000000] {error=-26880,SSL - No data of requested type currently available on underlying transport}'

I have attached the log, however the error is not reflected there: phantasm.log

The error has happened several times and at different times during the process so I am assuming that the problem is related to NCBI connection?

Can you please advise?

Thanks again.

dr-joe-wirth commented 1 year ago

This definitely looks like an issue with NCBI or your internet connection. I have seen problems with NCBI before. Let me know if this continues to happen and I'll try to implement a bug fix for the next release. If I were you, I'd try running it again and seeing if you still get the error. NCBI just might have been fussy that particular day.

dr-joe-wirth commented 1 year ago

going to close this out since I did not hear back from you. Feel free to reopen if the problem persists.