Unable to generate kmer.fa by FlagUniqueKmers.dll

[Aliyabai]

the kmer.fa generated by FlagUniqueKmers.dll is empty， even the inputFasta became empty.

$ mono ../src/Canvas/Tools/FlagUniqueKmers/FlagUniqueKmers.dll chr1.fa kmer.fa 2017/10/23 15:38:30 Start Load FASTA file at chr1.fa, write kmer-flagged output to kmer.fa 2017/10/23 15:38:30 >>>Pass 1: flagged 0 unique kmers

2017/10/23 15:38:30 Flagging complete 2017/10/23 15:38:30 Output written to kmer.fa

[jiao2017]

Me too, need help! I use the canvas 1.29 binary version.

[garrettjstevens]

@Aliyabai @jiao2017 I had this same problem (namely FlagUniqueKmers.dll produced an empty output file and deleted the contents of the input FASTA) with version 1.29.

I downloaded version 1.25 of Canvas and it seems to work fine. Hope this helps.

[eroller]

Thanks for the information. We will push out a new build this week.

[Aliyabai]

The FlagUniqueKmers.dll program uses lots of cpu almost 100% for a long time, does it has any other parameters?

在 2017年10月31日，01:16，Eric Roller notifications@github.com 写道：

Thanks for the information. We will push out a new build this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Illumina/canvas/issues/66#issuecomment-340517010, or mute the thread https://github.com/notifications/unsubscribe-auth/AOS6pdRd7B0vkB7k95EWSBP1YEMtTNRjks5sxgRSgaJpZM4QCarT.

[eroller]

This may be expected. How long has it been running for? FlagUniqueKmers.dll only needs to run once per reference genome. It does take a long time to run depending on the reference genome. We have hg38 and hg19 precomputed and available for download from S3.

[Aliyabai]

Several days and my servers were died. And I also can not find hg19 in S3, can you share it to me in another way. Thank you.

在 2017年11月23日，00:40，Eric Roller notifications@github.com 写道：

This may be expected. How long has it been running for? FlagUniqueKmers.dll only needs to run once per reference genome. It does take a long time to run depending on the reference genome. We have hg38 and hg19 precomputed and available for download from S3.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Illumina/canvas/issues/66#issuecomment-346406482, or mute the thread https://github.com/notifications/unsubscribe-auth/AOS6pUgBvNibqrGkhc90DRMyvANQ-Wr0ks5s5E6RgaJpZM4QCarT.

[eroller]

That seems a little too long, but we haven't benchmarked running under dotnet core on Linux so I can't say if that is expected. On Windows it shouldn't take that long.

You should be able to download all the hg19 files from S3 using wget:

wget http://canvas-cnv-public.s3.amazonaws.com/hg19/kmer.fa

the full list of available files is here: http://canvas-cnv-public.s3.amazonaws.com/

[Aliyabai]

Thanks very much, I downloaded the kmer.fa by wget.

Best wish ~

在 2017年11月23日，13:45，Eric Roller notifications@github.com 写道：

That seems a little too long, but we haven't benchmarked running under dotnet core on Linux so I can't say if that is expected. On Windows it shouldn't take that long.

You should be able to download all the hg19 files from S3 using wget:

wget http://canvas-cnv-public.s3.amazonaws.com/hg19/kmer.fa http://canvas-cnv-public.s3.amazonaws.com/hg19/kmer.fa the full list of available files is here: http://canvas-cnv-public.s3.amazonaws.com/ http://canvas-cnv-public.s3.amazonaws.com/ — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Illumina/canvas/issues/66#issuecomment-346535846, or mute the thread https://github.com/notifications/unsubscribe-auth/AOS6pUGTAVTgw2dLA3rRYcl2tsZMgMEpks5s5QaJgaJpZM4QCarT.