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Read Assembly and Annotation Pipeline Tool
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RAPT running problem #12

Open ssqd2022 opened 2 years ago

ssqd2022 commented 2 years ago

When I run RAPT, by the following command:

./run_rapt.py -a SRS10489852

I got the error in verbose.log: Found input: SRA run accession SRS10489852 Reference data presents and is intact, skip downloading ... SRA connection failed for accession SRS10489852:...

When, I run the recommended test code

./run_rapt.py -a SRR3496277

I met success and I see the assembly result.

I have tried several other SRA accession numbers. I got the same problem. Any comment or help will be appreciated.

thibaudnis commented 2 years ago

Thank you for trying RAPT! SRS10489852 is the identifier for a sample, which corresponds to multiple SRA experiements and runs. RAPT takes runs as input, with identifiers starting with the letters SRR, ERR or DRR. In addition, these runs must be of short reads (Illumina). See SRS10489852. Several experiments are linked to this sample, but the only one that was generated with an Illumina instrument is experiment SRX12530589/run SRR16250963 . Please try running RAPT with SRR16250963 and let us know how it goes.

thibaudnis commented 2 years ago

I tried running RAPT on SRR16250963. Unfortunately, the run failed in the assembly step. I suspect this is because this sample is a mixture. If you look in the analysis tab of this page, out of the 25% of reads that can be identified, 60% are predicted to be bacterial and most of the rest is eukaryotic.