Problem in indexing toplevel genome with HISAT2
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1
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4.8 years ago
Batu ▴ 240

As I mentioned in my old post, I was unable to index a toplevel genome (both unmasked and soft-masked) with HISAT2. I still have problems with that. I'm using command as below: hisat2-build -f Mus_musculus.GRCm38.dna.toplevel.fa.gz Cm3895_ht2/GRCm38

Firstly, it gives these warnings in lots of lines:

Warning: Encountered empty reference sequence
Warning: Encountered reference sequence with only gaps

and after some time, it gives an error as below:

Calculating joined length
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: 00:28:31
Error: Encountered internal HISAT2 exception (#1)
Command: hisat2-build --wrapper basic-0 -f Mus_musculus.GRCm38.dna.toplevel.fa.gz Cm3895_ht2/GRCm38 
Deleting "Cm3895_ht2/GRCm38.1.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.2.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.3.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.4.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.5.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.6.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.7.ht2" file written during aborted indexing attempt.
Deleting "Cm3895_ht2/GRCm38.8.ht2" file written during aborted indexing attempt.

Previously, I had no problem when using separate chromosome files. Is there anything I'm missing when using toplevel genome? Thanks...

RNA-Seq genome hisat2 hisat2-build index • 4.2k views
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2
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Guess you have the answer inside error log: 'Reference file does not seem to be a FASTA file'. Try to unpack the reference file to fasta format and run index build once again.

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0
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Yes, it worked after unpacking. Gzipped files normally work with main hisat2 command, therefore I couldn't think about this reason. Thank you...

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3
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4.8 years ago
Batu ▴ 240

It worked after unpacking the genome. I couldn't figure out that gzipped files won't work whereas they work with main hisat2 command. Problem solved!

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I encountered the same problem and solved it by unzipping genome file. Thank you for bringing this up as a question.

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