Closed ewallace closed 8 years ago
Hi @ewallace,
Sorry for the late response. Would you like to send me the files so that I can reproduce and fix the issue?
I released a new version of HISAT2 (2.0.4) three days ago, which may include some fixes for your issue. I'll close this thread and reopen if this issue still occurs.
In 2.0.4, I also get into the same trouble when I build index for Nicotiana benthamiana.
It's my command:
hisat2-build -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
but I get this information:
is not reverse-deterministic, so reverse-determinize... b.sh: line 1: 29864 Killed hisat2-build -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
my cluster have 500G memory, the hsat2-build would occupy up to 400G after warning up with "is not reverse-deterministic, so reverse-determinize" after scanning HISAT2's tutorial, I execute the command for two part:
hisat2-build -3 -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
hisat2-build -r -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
the first command which only build .3.ht2 and .4.ht2 is fine, but the second command also can't work, this is the error :
Error: Encountered internal HISAT2 exception (#1) Command: hisat2-build --wrapper basic-0 -r -p 12 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file} Deleting "Nb_genome.1.ht2" file written during aborted indexing attempt. Deleting "Nb_genome.2.ht2" file written during aborted indexing attempt. Deleting "Nb_genome.5.ht2" file written during aborted indexing attempt. Deleting "Nb_genome.6.ht2" file written during aborted indexing attempt. Deleting "Nb_genome.7.ht2" file written during aborted indexing attempt. Deleting "Nb_genome.8.ht2" file written during aborted indexing attempt.
I still get the same error with HISAT2 2.2.1 . Is there any reason or a workaround for this?
Hi,
When I run
hisat2-build -p 4 ${genome_file} ${index_file}
the index builds fine.However, when I use the same inputs but run:
hisat2-build -p 4 --ss ${ss_file} --exon ${exon_file} ${genome_file} ${index_file}
Then I get the error:
Now, this is clearly not an accurate error report as it's the same fasta file.
I'm happy to supply the input file if you want (this is yeast so takes ~1min to build index).
Thanks Edward