Fasta file error only when adding --ss and --exon inputs

[ewallace]

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:

...
Writing header
Reserving space for joined string
Joining reference sequences
Reference file does not seem to be a FASTA file
Time to join reference sequences: 00:00:00
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal HISAT2 exception (#1)
...

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

[infphilo]

Hi @ewallace,

Sorry for the late response. Would you like to send me the files so that I can reproduce and fix the issue?

[infphilo]

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.

[zhou-ran]

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.

[Nilaksha88]

I still get the same error with HISAT2 2.2.1 . Is there any reason or a workaround for this?