Cufflinks "GffObj::getSpliced() error: improper genomic coordinate"

[rflrob]

Cufflinks is giving me this error:

$ cufflinks -p 4 -o analysis-multi/CaS1A/ -u -N -b Reference/AAA/mel_only.fa -G Reference/AAA/mel_only.gtf analysis-multi/CaS1A/assigned_dmel_rescued.bam 
cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v2.0.2, which is the most recent release.
[11:37:09] Loading reference annotation and sequence.
GffObj::getSpliced() error: improper genomic coordinate 9757988 on dmel_U for FBtr0114250
$ grep -B 3 -A 3 FBtr0114250 Reference/AAA/mel_only.gtf 
dmel_U  FlyBase exon    9696725 9697478 .       -       .       transcript_id "FBtr0300169"; gene_id "FBgn0259871"; gene_name "Su(Ste):CR42440";
dmel_U  FlyBase exon    9700241 9701121 .       +       .       transcript_id "FBtr0300168"; gene_id "FBgn0259872"; gene_name "Su(Ste):CR42441";
dmel_U  FlyBase exon    9728301 9728935 .       -       .       transcript_id "FBtr0300170"; gene_id "FBgn0259873"; gene_name "Su(Ste):CR42442";
dmel_U  FlyBase exon    9757371 9757988 .       +       .       transcript_id "FBtr0114250"; gene_id "FBgn0085796"; gene_name "CR41539";
dmel_U  FlyBase exon    9795507 9796558 .       +       .       transcript_id "FBtr0114256"; gene_id "FBgn0085802"; gene_name "CR41548";
dmel_U  FlyBase exon    9807015 9808063 .       -       .       transcript_id "FBtr0114195"; gene_id "FBgn0085745"; gene_name "CR40565";
dmel_U  FlyBase exon    9812760 9813782 .       +       .       transcript_id "FBtr0300171"; gene_id "FBgn0259874"; gene_name "Su(Ste):CR42443";

I'm working on generating a minimal test set that reproduces the error, but in the mean time, does anyone have an idea what might be going on? The GTF file I'm using was generated directly from the FlyBase GFF file using:

gffread dmel-all-r5.46.gff -E -T -o- | awk '{print "dmel_"$0}' > mel_only.gtf

so if there's a problem with something, it seems unlikely I'm the only one who's seen it.


EDIT:

Looks like there was something wrong with the fasta index for the fasta file. Deleting that and letting it get rebuilt fixed the error.

[bharati]

Even I got this error
GffObj::getSpliced() error: improper genomic coordinate 19628622 on chrY for NR_028083

Same error (with the same coordinates) was there for two different samples, is there any problem with gtf file which was parsed with cufflinks or something else?

Please help me out I am stuck.

[pengchy]

EDIT:

Looks like there was something wrong with the fasta index for the fasta file. Deleting that and letting it get rebuilt fixed the error.

It works. thank you for your experience sharing.

[Paldito]

Still having the same error:

I am obtaining this error...

[14:48:47] Loading reference annotation.
[14:48:52] Inspecting reads and determining fragment length distribution.
Processed 146523 loci.
> Map Properties:
> Normalized Map Mass: 67542758.00
> Raw Map Mass: 67542758.00
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 186.60
> Estimated Std Dev: 78.33
[15:05:11] Assembling transcripts and estimating abundances.
Processed 146523 loci.
[17:24:06] Loading reference annotation and sequence.
GffObj::getSpliced() error: improper genomic coordinate 130018301 on chr10 for Olfr820

What should I do?
Both files where downloaded from UCSC servers and the mm10.2bit was converted to Fasta using twoBitToFa

Thank you!