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Gossamer bioinformatics suite
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Xenome doesnt finish - takes very long time #16

Closed obwan74 closed 6 years ago

obwan74 commented 6 years ago

Hi, I finished indexing the genomes. If I use -M 124 and high thread number somehow indexing keeps on going and doesnt finish. If I use low memory -M 64 and 8 threads indexing completed fairly fast.

However, for xenome classify whether I specify -M 100 or no -M option, xenome classify keeps on going and doesnt end. I checked the total number of reads from input fastq and they match total reads classified into host, graft, combined etc. bins. It appears xenome does not finish itself after classifying reads successfully. what could be the issue?

Deguerre commented 6 years ago

G'day. This is almost certainly the same problem as issue #9.

splaisan commented 6 years ago

I could also classify after some errors (mine) but classify hangs after finishing read classification with 0% activity and no summary produced. what can we use with -D to get more verbose debug output? Please help!

Deguerre commented 6 years ago

Definitely a duplicate of #9 .