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SRA to FASTQ error ：can't obtain technical reads files #990

Open Mollyx06 opened 2 days ago

Mollyx06 commented 2 days ago

Hello, I'm having some problems with the latest sratools (==3.1.1), the raw data was downloaded directly from NCBI via prefetch, and the data is labeled as double-ended sequencing data from illumina, but when I try to convert the format I always can't get the appropriate file, and when using fastq-dump image Only a fastq.gz ending in “1” is generated. Then I tried another tool, fasterq-dump, and followed the advice to add the --include-technical parameter, but it reported the error image Having used the --split-3 parameter before this I can only get one file, any other suitable suggestions? Here's a screenshot of the raw data image

wraetz commented 2 days ago

When you run fasterq-dump to include technical reads - it reacted with 'disk-limit exeeded'. The tool does a check if the expected size of the output will fit onto your HDD/SSD. It asked you to re-run the same command with the '-x' option ( aka print details ) - that will tell you why it rejected to do it. You can then lift the disk-limit with the '--disk-limit' option ( if you think you have enough space ) or turn the size-check off with '--size-check off'.

wraetz commented 2 days ago

The run-browser listed the number of bases as 26.3 GB. The expected output ( FASTQ ) is approximately 2.5 times that number.

durbrow commented 2 days ago

As you can see from your screenshot, the run has only one read. This is why you are getting only one file from fastq-dump. Please contact the SRA curators at sra@ncbi.nlm.nih.gov, and let them know that there's a problem with the data file.