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Question: Salmon error message
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I am trying to quantify the expression of my genes by using salmon. The command is following

salmon quant -p 10 -i ensembl_index/ -l A -1 SRR1056045_2.fastq.gz -2 SRR1056045_1.fastq.gz -o ensembl_quant

But got the following error message:

Error reading from the FASTA/Q stream. Minimum return code for left and right read was (-2). Make sure the file is valid.

I was trying to analyse 5 .sra files which were downloaded from ncbi. Two of my files were OK, but enter-count problems with rest three. Same error message for them. Is it the problem with those .sra files?

Thanks

ADD COMMENTlink 16 months ago saadleeshehreen • 60 • updated 16 months ago Devon Ryan 90k
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1

If you are worried about sra files, you can directly download your fastq.gz files here:

https://www.ebi.ac.uk/ena/data/view/SRR1056045

ADD REPLYlink 16 months ago
jomo018
• 480
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A couple things:

  1. One of those files (likely SRR1056045_1.fastq.gz) is corrupt. Just download it again.
  2. You flipped which file goes where. The _1 file should be with -1 and the _2 file should be with -2. Granted, salmon may figure out you've swapped things since you specified -l A, but there's no need to chance that.
ADD COMMENTlink 16 months ago Devon Ryan 90k

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