# Cuffmerge error: duplicate/invalid 'transcript' feature ID=Ma03\_t01040.3 **URL:** \ **Category:** Uncategorized\ **Tags:** tool-deprecated\ **Created:** [June 10, 2020, 12:14pm UTC](https://help.galaxyproject.org/t/cuffmerge-error-duplicate-invalid-transcript-feature-id-ma03-t01040-3/3883 "2020-06-10T12:14:41Z")\ **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 10, 2020, 12:14pm UTC](https://help.galaxyproject.org/t/cuffmerge-error-duplicate-invalid-transcript-feature-id-ma03-t01040-3/3883/1 "2020-06-10T12:14:41Z")
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/invalid ‘transcript’ feature ID=Ma03\_t01040.3 [FAILED] Error: could not execute cuffcompare i could not understant how to resolve can you please explain me clearly. ---
**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, 10:41pm UTC](https://help.galaxyproject.org/t/cuffmerge-error-duplicate-invalid-transcript-feature-id-ma03-t01040-3/3883/2 "2020-06-11T22:41:11Z")
Hi @tikshana_yadav Some `gff3` datasets are released by data providers that contained duplicated “ID” identifiers. These cause problems with almost all tools. Using `gtf` annotation is a better choice. Please note that the tools you are using are deprecated. Details, reasons, and 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. 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 12, 2020, 2:20am UTC](https://help.galaxyproject.org/t/cuffmerge-error-duplicate-invalid-transcript-feature-id-ma03-t01040-3/3883/3 "2020-06-12T02:20:22Z")
Thank you for your kind information. Can you please suggest me some tools to get differential expression of genes in Musa balbisiana with non replicated data which has to annotated with Musa accuminata ---
**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, 9:06am UTC](https://help.galaxyproject.org/t/cuffmerge-error-duplicate-invalid-transcript-feature-id-ma03-t01040-3/3883/4 "2020-06-18T09:06:31Z")
Thank you all for your kind help. I simply want to suggest the future that if this sort of error will occur just check whether your input file is correct or not go through each and every location and check the path as well as your file name. Just keep everything simple do not complex anything. This is what I resolved these days. A small mistake in your command may hamper your time and experiment. In short my bam file in samtools was not created properly so I run all command again and checked my path that resolved my issue/error. If you face the same just go through it make it SIMPLE