habilzare
commented
5 years ago I got the same error and a segmentation fault while processing single-read data using salmon 0.10.2. My command was:
salmon quant -i <transcripts_index_folder> -l A -r <some_R1.fastq> -o <output_quant_folder>
Are Salmon working on this since August?
Update: Using Salmon version 0.11.4 solved the issue for me.
Dear salmon authors,
While I was using salmon (v0.11.0, downloaded executable, on a Ubuntu Linux server) to process a single-end RNA-seq library, it reported the following error message:
"[ERROR] Transcript IDs are not in sorted order; please report this bug on GitHub!"
Actually I found it reports this error message for over tens of millions of times through greping the log file. And the command line I applied to invoke salmon was like this:
"salmon quant -i mySalmonIndexFile(FMD based/transcriptome) -l A -r myLibrary.fastq -p 8"
It looks like this is something about single-end reads processing, since I arbitrarily picked up another pair-end library, which works prefectly fine with command line "-1 PE_library_1.fastq -2 PE_library_2.fastq", however, when I deliberately provide only one end of the library with "-r PE_library_1/2.fastq", exactly the same error was recurred immediately.
Curiously, salmon could still accomplish the whole procedure and generate the results file with the aformentioned error reported. But I' m worried about its reliability in this situation.
I' m wondering if you have any clues about this issue. With many thanks ahead!