Question: Error with DESeq2 with Kallisto abundance.tsv input
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florian.uellendahl • 0 wrote:
Hello everyone, I'm trying to run DESeq2 (Galaxy Version 2.11.40.2) on Kallisto abundance.tsv data with a tabular file for transcript to gene mapping (t2g). I always get this error:
Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read.delim (install 'readr' package for speed up)
1 Error in infRepImporter(dirname(files[i])) :
reading kallisto results from hdf5 files requires Bioconductor package `rhdf5`
Calls: tximport -> infRepImporter
If I use a .gtf file, then I get this:
Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read.delim (install 'readr' package for speed up)
1 Error in infRepImporter(dirname(files[i])) :
reading kallisto results from hdf5 files requires Bioconductor package `rhdf5`
Calls: tximport -> infRepImporter
Warning message:
In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
Switching back to Galaxy Version 2.11.39 doesn't give an error, but finishes after the same time with an empty result file. Because you'd typically assume a wrong input, I tried several alternative formats for the t2g table, with quotes, without, tab or comma separated and so on. I removed the transcript-IDs' version tags in the abundance.tsv to match the ones in the t2g files. So I have three questions:
- Which one is the correct input type for kallisto results and the t2g table in Galaxy DESeq2?
- Is there a known bug that I'm running into that I haven't found?
- Could renaming the files from abundance.tsv to e.g. abundance01.tsv be the source of the problem?
Thank you in advance for help with this one! Florian Uellendahl-Werth
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modified 8 weeks ago
by
Jennifer Hillman Jackson ♦ 25k
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written
9 weeks ago by
florian.uellendahl • 0
This error is due to a server-side issue with the installed dependencies for the tool. If working at https://usegalaxy.org, please know we are working to fully characterize and fix the issue. More feedback soon.
Meanwhile, try running the tool at https://usegalaxy.eu. I'll be testing with Kallisto inputs there as well when working out the scope of the problem. The reference data (GTF or tabular) is not a factor.
Thanks! Jen, Galaxy team