Exception : [Error: RapMap-based indexing is not supported in this version of salmon.]

[Arturo3116]

I'm trying to use Trinity With the modules: module load trinityrnaseq/2.6.2 module load samtools/1.16 module load jellyfish/2.3.0 module load jdk/1.8.0_151 module load bowtie2/2.2.9 module load salmon/1.9.0 But I get the error: Exception : [Error: RapMap-based indexing is not supported in this version of salmon.] salmon index was invoked improperly. For usage information, try salmon index --help Exiting. Error, cmd: salmon index -t /work/luarrieta/proy_labap/Output/trinity/read_partitions/Fb_0/CBin_36/c3679.trinity.reads.fa.out/Trinity.fasta.tmp -i /work/luarrieta/proy_labap/Output/trinity/read_partitions/Fb_0/CBin_36/c3679.trinity.reads.fa.out/Trinity.fasta.tmp.salmon.idx --type quasi -k 25 -p 1 died with ret (256) at /opt/bioinf/trinityrnaseq-2.6.2/util/support_scripts/../../PerlLib/Process_cmd.pm line 19. Process_cmd::process_cmd('salmon index -t /work/luarrieta/proy_labap/Output/trinity/rea...') called at /opt/bioinf/trinityrnaseq-2.6.2/util/support_scripts/salmon_runner.pl line 20 Trinity run failed. Must investigate error above.

@brianjohnhaas

[rob-p]

I am not sure how the index here was created, but the actual error signifies that you are attempting to quantify the assembled transcripts using a recent version of salmon (1.9.0 in this case) against an index that was created by a very old version of salmon (pre 1.0). This is not supported, as the index format completely changed between pre v1.0 and post v1.0, and newer versions rely on a completely different data structure.

[brianjohnhaas]

Hi all - this looks like an old version of Trinity. I'd suggest upgrading.

For any version of Trinity, you can look at the Dockerfile to see what the corresponding compatibilities are for versions that get co-installed for a fully functional package. For example, in the current release, you'll find:

https://github.com/trinityrnaseq/trinityrnaseq/blob/5ce78d2b6d63aaae9fe491408311ebaf158deaa6/Docker/Dockerfile#L235

best,

~brian

On Fri, Feb 24, 2023 at 1:19 PM Rob Patro @.***> wrote:

I am not sure how the index here was created, but the actual error signifies that you are attempting to quantify the assembled transcripts using a recent version of salmon (1.9.0 in this case) against an index that was created by a very old version of salmon (pre 1.0). This is not supported, as the index format completely changed between pre v1.0 and post v1.0, and newer versions rely on a completely different data structure.

— Reply to this email directly, view it on GitHub https://github.com/COMBINE-lab/salmon/issues/832#issuecomment-1444189059, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5M6TN6DEQJQCP2AALWZD3TRANCNFSM6AAAAAAVHFUQRA . You are receiving this because you were mentioned.Message ID: @.***>

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[imyingchulo]

Hello, Thank you for your guidance on this question. However, I encountered the same error despite using the latest versions of Trinityrnaseq and salmon.

I ran Trinity version 2.15.1 to generate Fasta files. I attempted to use Salmon version 1.10.1 for indexing, but I encountered this exception. Upon checking the Docker link provided in the comment, I found that the salmon version listed is 1.5.0. So, I tried using Salmon 1.5.0 and encountered the same error. Could you please advise me on how to resolve this issue? Thank you.

$./trinityrnaseq-v2.15.1/Trinity  --seqType fq --max_memory 6 --samples_file sample.txt --min_kmer_cov 2 --no_parallel_norm_stats --output trinity_test_0210_1019 --CPU 6

...

$ ~/tools/salmon-latest_linux_x86_64/bin/salmon index --index quasi --type quasi --transcripts ~/first_try_Gall/trinity_test_0210_1019.Trinity.fasta 
Version Info: This is the most recent version of salmon.
Exception : [Error: RapMap-based indexing is not supported in this version of salmon.]
/home/ubuntu/tools/salmon-latest_linux_x86_64/bin/salmon index was invoked improperly.
For usage information, try /home/ubuntu/tools/salmon-latest_linux_x86_64/bin/salmon index --help
Exiting.