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DaehwanKimLab / hisat

Fast spliced aligner with low memory requirements
http://www.ccb.jhu.edu/software/hisat
GNU General Public License v3.0
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segmentation fault on flybase data #3

Open antonkulaga opened 9 years ago

antonkulaga commented 9 years ago

I managed to successfully build and index with ( ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.04_FB2015_01/fasta/dmel-all-chromosome-r6.04.fasta.gz ) and version 0.1.5-beta (the one from the site, I did not check the github version).

But when I type "hisat_inspect --summary" I get "segmentation fault error". If needed I can share a ftp folder with my index, but I suspect it is an issue with assembling data from flybase reference genomes.

antonkulaga commented 9 years ago

What is interesting is that even with "segmentation fault" index I managed to build strintie GTFs (alghough with a lot of warnings)

infphilo commented 9 years ago

Hi Anton,

Someone already reported this problem to me before you, and I fixed it. Would you like to use this GitHub version of HISAT? You don't need to rebuild the fly related sequences as there was no issue with hisat-build.

Thanks, Daehwan

antonkulaga commented 9 years ago

After compilation from hisat whenever I use hisat I get

(ERR): hisat-align exited with value 1

I have such problem on two configuration: (CentOS and Linux Mint/Ubuntu)

antonkulaga commented 9 years ago

I checked, with a version from git hisat-summary seems to work fine. Have you fixed only summary problem or there was also something else with index building, so I should rebuild my indexes?

huangfei304 commented 9 years ago

I also have the problem with run hisat -x referenece_genome -1 read1.fq -2 read2.fq " the error is "(ERR): hisat-align died with signal 11 (SEGV) (core dumped)".