Salmon_index.json doesn't seem to exist

Question

[dylannicoembros]

Good evening, thanks to a previous post I was able to solve one problem in my pipeline. Now I am dealing with another one. I have to quantify some rna sequence with salmon and I downloaded a pre-computed index from the link suggested in salmon documentation. The link is this, I downloaded the salmon_

http://refgenomes.databio.org/v3/genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4

Now, I am trying to run this command to quantify:

salmon quant -i salmon_partial_sa_index\?tag\=default -l A -1 P10_1.fq.gz -2 P10_2.fq.gz --validateMappings -o transcripts_quant

where salmon_partial_sa_index\?tag\=default refers to the downloaded index, and P10_1.fq.gz -2 P10_2.fq.g to the paired reads.

The error that I get it's the following:

The index version file salmon_partial_sa_index?tag=default/versionInfo.json doesn't seem to exist.  Please try re-building the salmon index

It's worth mentioning that I am working directly on a remote server and I downloaded the pre-build index with the wget command, in the same folder as the paired reads. I read online for some memory space troubles, but I think I have more than 100GB on the server, so I do not think that this is the issue.

Also, the format of the index is gzip compressed data but somehow, after the download, it is saved with that strange name.

Thank you very much for the help. I'll be avaiable for quick responses.

Answer 1

[ATpoint]

When I download this tarball (tgz) I get salmon_partial_sa_index__default.tgz. This one unpacks with tar zxvf salmon_partial_sa_index__default.tgz and then a folder default is returned. This is what the -i takes as input. Seems your download was corrupted, or incorrectly unpackaged, or wrong path.

[dylannicoembros]

I will try and let you know. Thank you!

[dylannicoembros]

I decompressed it and still not working. Now I get the error message :Exception : [rapidjson internal assertion failure: IsObject()

[ATpoint]

wget http://awspds.refgenie.databio.org/refgenomes.databio.org/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_partial_sa_index__default.tgz
tar zxvf salmon_partial_sa_index__default.tgz
atpoint@DESKTOP-O7JK99H:~$ ls default/
2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.gtf  ctable.bin       decoys.txt              gentrome.fa  mphf.bin  pre_indexing.log  refAccumLengths.bin  reflengths.bin  seq.bin
complete_ref_lens.bin                                 ctg_offsets.bin  duplicate_clusters.tsv  info.json    pos.bin   rank.bin          ref_indexing.log     refseq.bin      versionInfo.json

...cannot help beyond that.

[dylannicoembros]

Thank you. I really appreciate