Genome Version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a

[meherpreethi777]

Description of the bug

While running RNAvar pipeline and providing the reference as a GTF file, the following error was seen:
EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a
SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a

In order to overcome the compatibility issue, the --star_index flag was removed and RNAvar was re-run.
Based on the log file, as indicated in the documentation, the pipeline tried to build in it's own STAR indices using "genomeGenerate" but then ran into the same error:

EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a
SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a

Command used and terminal output

nextflow rnavar/main.nf \
        --input samplesheet.txt \
        --outdir <output> \
        --gtf Homo_sapiens.GRCh38.104.gtf \
        --fasta Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz \
        --known_indels resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz \
        --known_indels_tbi resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz.tbi \
        --seq_center "Core facility"

Relevant files

No response

System information

No response

[Shaun-Regenbaum]

Is there a reason this is commented out in prepare_genome.nf?
if((!ch_star_index) || getIndexVersion(ch_star_index) != '2.7.4a'){ ch_star_index = STAR_GENOMEGENERATE(ch_fasta,ch_gtf).index ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) }

as long as generategenome is in the modules, it will solve this issue. I can submit a PR for this too if we want.

[Shaun-Regenbaum]

@maxulysse Let me know your thoughts or perhaps you have already done this in dev?

[maxulysse]

Is there a reason this is commented out in prepare_genome.nf? if((!ch_star_index) || getIndexVersion(ch_star_index) != '2.7.4a'){ ch_star_index = STAR_GENOMEGENERATE(ch_fasta,ch_gtf).index ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) }

I think we commented this because we never really managed to make it work

as long as generategenome is in the modules, it will solve this issue. I can submit a PR for this too if we want.

[Shaun-Regenbaum]

Oh I can add it to my PR as I already did that. I am a bit busy, but will submit a new PR with linting and everything later this week or next week.

…

On Mon, Jan 8, 2024 at 5:27 PM Maxime U Garcia ***@***.***> wrote: Is there a reason this is commented out in prepare_genome.nf? if((!ch_star_index) || getIndexVersion(ch_star_index) != '2.7.4a'){ ch_star_index = STAR_GENOMEGENERATE(ch_fasta,ch_gtf).index ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) } I think we commented this because we never really managed to make it work as long as generategenome is in the modules, it will solve this issue. I can submit a PR for this too if we want. — Reply to this email directly, view it on GitHub <#92 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADANAZH4GPPKSAORGY3SXLDYNQF4XAVCNFSM6AAAAAAYVUZTN2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBRGIZDMOJYGI> . You are receiving this because you commented.Message ID: ***@***.***>

[bleazard]

We have also encountered this error. Do you know if there is a solution that we can use? We got the error as with the user above, when specifying our own fasta and gtf files and without the star_index flag.

[KristinaGagalova]

I am echoing the previous posts, I encountered the same error. I used gtf and Fasta files as input, and no star_index flag

[ERIGR]

Hi, I'm encountering the same problem. Is there any way to solve this issue easily ?

[KristinaGagalova]

@ERIGR you can generate the index with STAR 2.7.9 and pass it to rnavar with the option --star_index