errors

[Ferdinand Marlétaz]

Hi - 

I am attempting to use GRIT to build gene models for the genome an alternative model system in which we have a wealth of stranded RNAseq and CAGE-seq. I launched it with the command: 

run_grit --verbose --ucsc -t 16 \
--use-reference-junctions  --use-reference-tes-exons \
--reference Bla_annot_cuff2.gtf --fasta Bl71nemr.fa \
--rnaseq-reads /home/zoo/zool1048/Amphioxus/mappedRNAseq/Embr_8h_a_star.bam \
--cage-reads /home/zoo/zool1048/Amphioxus/runGRIT/Embr_8h_CAGE.srt.bam

I got multiple error messages, as the following one (~100,000), I suspect it is a problem with the parsing of provided gtf file, but I am not sure. To be sure if the problem is with mhy data or with my installation, I wanted to download the example dataset at http://grit-bio.org/GRIT_example.tar.gz but it not available anymore (the server seems down). In the created output folder (./discover), I got some files, such as 'None.gtf' but they are empty.

I would really appreciate some feedback to be able to configure and run GRIT properly, because the paper sounds really interesting. 

Best

Ferdinand 

Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1120, in find_exons_worker
 rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1038, in find_exons_in_gene
 gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 580, in build_splice_graph_and_binned_reads_in_gene
 ) = extract_jns_and_paired_reads_in_gene(gene, rnaseq_reads)
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 483, in extract_jns_and_paired_reads_in_gene
 (gene.chrm, gene.strand, region.start, region.stop), reads)
ValueError: too many values to unpack