# getSpliced() error: improper genomic coordinate 46954453 on chrUn\_random for TCONS\_00084296 **URL:** \ **Category:** Uncategorized\ **Tags:** tool-deprecated, reference-annotation, queued-gray-datasets, reference-genome, paused-jobs\ **Created:** [June 11, 2020, 8:30am UTC](https://help.galaxyproject.org/t/getspliced-error-improper-genomic-coordinate-46954453-on-chrun-random-for-tcons-00084296/3889 "2020-06-11T08:30:39Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![tikshana\_yadav](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/tikshana_yadav/32/1605_2.png) [@tikshana\_yadav](https://help.galaxyproject.org/u/tikshana_yadav)\ **Post date:** [June 11, 2020, 8:30am UTC](https://help.galaxyproject.org/t/getspliced-error-improper-genomic-coordinate-46954453-on-chrun-random-for-tcons-00084296/3889/1 "2020-06-11T08:30:39Z")
I have searched through all the threads on this topic and I have yet to find a reasonable explanation for why I continue to encounter this error. I have already run Cufflinks on my samples, but when I attempt to run Cuffmerge (cuffdiff -o /scratch/sbag/Tikshana/BANANA/cuff/Macbal\_diff -b /scratch/sbag/Tikshana/BANANA/RAW/Mac.fa -p 8 -u /scratch/sbag/Tikshana/BANANA/cuff/merged\_asm/merged.gtf -L leaf,root /scratch/sbag/Tikshana/BANANA/map/Top\_Macbal\_6127/accept ed\_hits.bam, /scratch/sbag/Tikshana/BANANA/map/Top\_Macbal\_6141/accepted\_hits.bam), I get the following error: Error (GFaSeqGet): end coordinate (46954453) cannot be larger than sequence length 46622217 GffObj::getSpliced() error: improper genomic coordinate 46954453 on chrUn\_random for TCONS\_00084296 PLEASE HELP ME TO CLEAR THIS… ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [June 11, 2020, 10:54pm UTC](https://help.galaxyproject.org/t/getspliced-error-improper-genomic-coordinate-46954453-on-chrun-random-for-tcons-00084296/3889/2 "2020-06-11T22:54:31Z")
@tikshana_yadav > [@tikshana\_yadav](#): > > improper genomic coordinate 46954453 on chrUn\_random This problem looks like a genome mismatch issue. Data was mapped against one version of the genome but the annotation was based on a different one? My guess is both happened to have a “chrUn\_random” chromosome but they are different lengths, which means different content. All of the coordinates in your data will be wrong if this is true – and the tool will not necessarily error, just produce scientifically incorrect results. That said, all of these tools are deprecated when used in Galaxy, as explained in your other post here: > [@Cuffmerge error: duplicate/invalid 'transcript' feature ID=Ma03\_t01040.3](https://help.galaxyproject.org/t/cuffmerge-error-duplicate-invalid-transcript-feature-id-ma03-t01040-3/3883): > > I have searched through all the threads on this topic and I have yet to find a reasonable explanation for why I continue to encounter this error. I have already run Cufflinks on my samples, but when I attempt to run Cuffmerge (cuffmerge -p 8 -g /scratch/sbag/Tikshana/BANANA/RAW/Mac.gff3 -s /scratch/sbag/Tikshana/BANANA/RAW/Mac\_genome.fa /scratch/sbag/Tikshana/BANANA/cuff/assemblies\_Macbal.txt -o /scratch/sbag/Tikshana/BANANA/cuff/Macbal\_merge), I get the following error: GFF Error: duplicate/in… Why and the alternatives are covered in this prior Q&A: > [@Cuff Suite Not Running -- Deprecated Tool Suite](https://help.galaxyproject.org/t/cuff-suite-not-running-deprecated-tool-suite/2298): > > Cufflinks, Cuffcompare, and Cuffnorm stopped running. I tried resume paused jobs but still paused. If you want to try to troubleshoot line-command usage, there was a google group – I don’t think it is very active anymore but you may find prior help. Biostars, Seqanswers, and other general bioinformatics forums will also have much prior discussion. These are usually common enough that even just a basic web search with the error message quoted will find help. But avoid using the tools in Galaxy, or expected problems. Thanks! ---
**Author:** ![tikshana\_yadav](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/tikshana_yadav/32/1605_2.png) [@tikshana\_yadav](https://help.galaxyproject.org/u/tikshana_yadav)\ **Post date:** [June 18, 2020, 9:11am UTC](https://help.galaxyproject.org/t/getspliced-error-improper-genomic-coordinate-46954453-on-chrun-random-for-tcons-00084296/3889/3 "2020-06-18T09:11:32Z")
Solved by checking all paths and file name, one negligible mistake might abandon the whole experiment. Make it simple by checking all file name and location is deeply suggested ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2026, 6:39am UTC](https://help.galaxyproject.org/t/getspliced-error-improper-genomic-coordinate-46954453-on-chrun-random-for-tcons-00084296/3889/4 "2026-03-17T06:39:22Z")