20161111|121503| 46693| ERROR: mummer and/or mgaps returned non-zero

PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study

BSD 3-Clause Clear License

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20161111|121503| 46693| ERROR: mummer and/or mgaps returned non-zero #50

Closed danshu closed 8 years ago

danshu commented 8 years ago

Hi,

I have finished 3-unzip and have output files uner "3-unzip". However, I just noticed that for many contig directories under "/data/jellyfish/Pacbio/falcon/san_falcon_t7_run3/3-unzip/1-hasm", I have "nucmer.error" files, which have error messages like "20161111|121503| 46693| ERROR: mummer and/or mgaps returned non-zero". What does these errors mean? Will they influence the results of 3-unzip?

Best, Quan

pb-jchin commented 8 years ago

you can ignore some nucmer error. This code is still in its early stage, some boundary cases are not check before sending to nucmer and we might eventually replace nucmer by something else.