# FLAIR app returning 0 lines of output

**URL:** <https://help.galaxyproject.org/t/flair-app-returning-0-lines-of-output/14678>\
**Category:** usegalaxy.eu support\
**Tags:** troubleshooting\
**Created:** [February 7, 2025, 1:57am UTC](https://help.galaxyproject.org/t/flair-app-returning-0-lines-of-output/14678 "2025-02-07T01:57:19Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![LukaDM](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/lukadm/32/6734_2.png) [@LukaDM](https://help.galaxyproject.org/u/LukaDM)\
**Post date:** [February 7, 2025, 1:57am UTC](https://help.galaxyproject.org/t/flair-app-returning-0-lines-of-output/14678/1 "2025-02-07T01:57:19Z")

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Hello. I’m trying to use the FLAIRcorrect tool to correct splice site calls in a cDNA alignments from a nanopore dataset. The tool is returning 0 lines of data. The job information shows the following:

Tool standard output: [E::fai\_build3\_core] Failed to open the file reference.fa  
[faidx] Could not build fai index reference.fa.fai

Tool standard error: Error running samtools faidx for indexing fasta reference for flair  
index file reference.fa.fai not found, generating…  
WARNING. chromosome (chrX) was not found in the FASTA file. Skipping.

Step 1/5: Splitting junctions from GTF by chromosome: 0%| | 0/13 [00:00\<?, ?it/s]e[A  
Step 1/5: Splitting junctions from GTF by chromosome: 100%|██████████| 13/13 [00:00\<00:00, 49122.48it/s]

Step 3/5: Preparing annotated junctions to use for correction: 0%| | 0/1 [00:00\<?, ?it/s]e[A  
Step 3/5: Preparing annotated junctions to use for correction: 100%|██████████| 1/1 [00:00\<00:00, 203.40it/s]

Step 4/5: Preparing reads for correction: 0it [00:00, ?it/s]e[A

Step 4/5: Preparing reads for correction: 38571it [00:00, 384514.92it/s]e[A  
Step 4/5: Preparing reads for correction: 39522it [00:00, 387437.99it/s]

Step 5/5: Correcting Splice Sites: 0it [00:00, ?it/s]e[A  
Step 5/5: Correcting Splice Sites: 0it [00:00, ?it/s]

Can someone interpret the output and error to tell me if the tool is running correctly? I get a similar output whether I use a reference fasta file from the single gene I’m analyzing, or using the locally cached hg38 assembly.

Could the 0 line output result from insufficient number of input alignments? My bed12 file has 39,000 regions.

Thanks in advanced for any insight.

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**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:** [February 11, 2025, 12:25am UTC](https://help.galaxyproject.org/t/flair-app-returning-0-lines-of-output/14678/2 "2025-02-11T00:25:12Z")

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Welcome, @LukaDM

You seem to be having a chromosome mismatch type of problem.

These guides below explain how to check and make adjustments, and you are welcome to share back more details for more specific help. See the banner at this forum for how to share. The history share link and any supplemental screenshots can be posted back here in your reply.

- [Reference genomes at public Galaxy servers: GRCh38/hg38 example](https://help.galaxyproject.org/t/reference-genomes-at-public-galaxy-servers-grch38-hg38-example/11616)

- [Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at](https://help.galaxyproject.org/t/custom-genome-custom-build-how-to-use-a-genome-that-is-not-natively-indexed-at-the-server-you-are-working-at/10082)

Let’s start there, and if you solve this, let us know! 🙂