Error: Encountered exception: 'Nongraph exception` when building index from TransDecoder

[jolespin]

I made the exons and splice-sites files. However, the splice-sites file was empty so I excluded it. I got the same error when including the splice-site file too tho.

Any thoughts?

Command:

source activate hisat2_env && hisat2-build --ss Transcriptome/transdecoder_output/splice_sites.txt --exon Transcriptome/transdecoder_output/exons.txt --seed 0 -p ${N_JOBS} Transcriptome/rnaspades_output/transcripts.fasta Transcriptome/rnaspades_output/transcripts.fasta

Log:

Settings:
  Output files: "Transcriptome/rnaspades_output/transcripts.fasta.*.ht2"
  Line rate: 7 (line is 128 bytes)
  Lines per side: 1 (side is 128 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  Transcriptome/rnaspades_output/transcripts.fasta
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:03
  Time to read SNPs and splice sites: 00:00:48
Warning: no variants or splice sites in this graph
Total time for call to driver() for forward index: 00:02:02
Error: Encountered exception: 'Nongraph exception'
Command: hisat2-build --wrapper basic-0 --ss Transcriptome/transdecoder_output/splice_sites.txt --exon Transcriptome/transdecoder_output/exons.txt --seed 0 -p 4 Transcriptome/rnaspades_output/transcripts.fasta Transcriptome/rnaspades_output/transcripts.fasta
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.1.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.2.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.3.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.4.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.5.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.6.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.7.ht2" file written during aborted indexing attempt.
Deleting "Transcriptome/rnaspades_output/transcripts.fasta.8.ht2" file written during aborted indexing attempt.

[parkchanhee]

@jolespin

The splice-site file should not be empty if you want to build a transcript index.

[jolespin]

That makes sense. I used TransDecoder so there weren't any introns for splice sites in the gff3 that was generated. In future version, would it be possible to use the "regular" hisat2 indexing method when the splice sites are empty? The exon positions were still available (though, just single exons) so this could be automated in a pipeline. I'm trying to find a good aligner for a pipeline I'm working on at JCVI that can be used in (mostly) all scenarios and HISAT2 seems to meet the critiera. If not, I can make some adjustments for the pipeline to incorporate these types of situations. Thanks!