Question

Cannot find header.json in salmon index directory

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mico • 0

@mico-15362

Last seen 9 months ago

United States

I am running tximeta to import the salmon quantification data. When I link to the transcriptome using the following code:

indexDir <- file.path(dir, "transcriptome", "GRCh38.index")
fastaPath <- c(file.path(dir, "transcriptome", "Homo_sapiens.GRCh38.cdna.all.fa.gz"),
               file.path(dir, "transcriptome", "Homo_sapiens.GRCh38.ncrna.fa.gz"))
gtfPath <- file.path(dir, "transcriptome", "Homo_sapiens.GRCh38.98.gtf.gz")

makeLinkedTxome(indexDir=indexDir,
                source="Ensembl",
                organism="Homo sapiens",
                release="98",
                genome="GRCh38",
                fasta=fastaPath,
                gtf=gtfPath,
                write=FALSE)

an error occurs:

Error: lexical error: invalid char in json text.
                                      ~/utr/transcriptom
                    (right here) ------^

The GRCh38.index is from salmon:

salmon index -t Homo_sapiens.GRCh38.cdna.all.fa.gz Homo_sapiens.GRCh38.ncrna.fa.gz -i GRCh38.index

I found there are only two json files in the index directory: info.json and versionInfo.json, and there is no file called header.json, which is necessary in the makeLinkedTxome function. Then I just create a header.json file using the information from info.json, and it seems work.

Did I miss some steps in salmon?

salmon tximeta rna-seq • 3.5k views

ADD COMMENT • link 5.1 years ago • updated 5.0 years ago mico • 0

score 1 · Accepted Answer · 2019-11-12

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Michael Love 43k

@mikelove

Last seen 19 hours ago

United States

What version of Salmon are you using?

ADD COMMENT • link 5.1 years ago Michael Love 43k

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The latest one, v1.0.0

ADD REPLY • link 5.1 years ago mico • 0

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Thanks for the bug report. I'll push a fix to the release branch today. The information has moved as you said from header.json to info.json in the index and so I'll just need a line to check both places.

ADD REPLY • link 5.1 years ago Michael Love 43k

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BTW, if I push a fix today, it should show up in the release branch by noon tomorrow (or the next day if something goes wrong).

ADD REPLY • link 5.1 years ago Michael Love 43k

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Great, thanks so much Michael!

ADD REPLY • link 5.1 years ago mico • 0

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We had to make one more change (Charlotte spotted the issue), so it will be fixed in v1.4.2, which should be available tomorrow. Relevant PR:

https://github.com/mikelove/tximeta/pull/22

You can also test the solution with:

devtools::install_github("mikelove/tximeta")

ADD REPLY • link 5.1 years ago Michael Love 43k

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Hi Michael, I tried Salmon v1.0.0 with decoy-augmented transcriptomes today and when I imported using tximeta v1.5.6 the same error occurred...

All files listed in the Salmon index directory:

complete_ref_lens.bin
ctable.bin
ctg_offsets.bin
duplicate_clusters.tsv
eqtable.bin
info.json
mphf.bin
pos.bin
pre_indexing.log
rank.bin
refAccumLengths.bin
ref_indexing.log
reflengths.bin
refseq.bin
seq.bin
versionInfo.json

ADD REPLY • link 5.0 years ago mico • 0

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Can you type out makeLinkedTxome in the console, type return and see what the code says?

The first line should be

indexJson <- file.path(indexDir, "info.json")

So I'm confused by it wouldn't be picking it up.

You can also run this line of code to check:

file.exists(file.path(indexDir, "info.json"))

ADD REPLY • link 5.0 years ago Michael Love 43k

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Hi Michael,

I am also using Salmon 1.0.0 and I am having the same issue after installing the version of tximeta from your github repository.

other attached packages: [1] tximeta_1.5.6

The first line of the function still looks for header.json

> makeLinkedTxome
function (indexDir, source, organism, release, genome, fasta, 
    gtf, write = TRUE, jsonFile) 
{
    indexList <- fromJSON(file.path(indexDir, "header.json"))
    indexSeqHash <- indexList$value0$SeqHash
    index <- basename(indexDir)
    std.sources <- c("Gencode", "Ensembl")
    for (src in std.sources) {
        if (tolower(source) == tolower(src)) {
            source <- src
        }

I actually only came across tximeta in the hopes that it won't crash unexpectedly as tximport is currently doing when trying to summarize lengths of ~80 samples.... :\

ADD REPLY • link 5.0 years ago rbenel ▴ 40

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So that first line doesn’t match the code thats in GitHub or Bioconductor, meaning you don’t yet have the fixed version of the code. I wonder what could be going on. Maybe try restarting R?

Re: 80 samples, tximeta calls tximport so no it won’t change performance. Make sure you’ve allocated sufficient memory — 200,000 x 80 x 3 is not a trivial amount of data.

ADD REPLY • link 5.0 years ago Michael Love 43k

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> makeLinkedTxome
function (indexDir, source, organism, release, genome, fasta, 
    gtf, write = TRUE, jsonFile) 
{
    indexJson <- file.path(indexDir, "info.json")
    if (!file.exists(indexJson)) {
        indexJson <- file.path(indexDir, "header.json")
    }
    indexList <- fromJSON(indexJson)
...

Yes the first line is looking for info.json, and you are right, R needs to restart after installing the latest tximeta then everything is OK... Many thanks!

ADD REPLY • link 5.0 years ago mico • 0