Comments (4)
Hi @ewallace,
Sorry for the late response. Would you like to send me the files so that I can reproduce and fix the issue?
from hisat2.
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.
from hisat2.
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.
from hisat2.
I still get the same error with HISAT2 2.2.1 . Is there any reason or a workaround for this?
from hisat2.
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