prefetch: cannot get remote location for RefSeq contig

[mikecuoco]

Hi I'm trying to download SRR11947587 and am getting the following response

$ prefetch -X u SRR11947587

2022-08-30T15:59:20 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-08-30T15:59:20 prefetch.3.0.0: 1) Downloading 'SRR11947587'...
2022-08-30T15:59:20 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-08-30T15:59:20 prefetch.3.0.0:  Downloading via HTTPS...
2022-08-30T16:17:28 prefetch.3.0.0:  HTTPS download succeed
2022-08-30T16:17:41 prefetch.3.0.0:  'SRR11947587' is valid
2022-08-30T16:17:41 prefetch.3.0.0: 1) 'SRR11947587' was downloaded successfully
2022-08-30T16:18:30 prefetch.3.0.0: 'SRR11947587' has 22 unresolved dependencies
2022-08-30T16:18:30 prefetch.3.0.0 int: connection unexpected while executing query within virtual file system module - cannot get remote location for 'NC_000067.6'

From running prefetch again on the downloaded sra file, I get the following

$ prefetch -X u SRR11947587/SRR11947587.sra 

2022-08-30T16:18:54 prefetch.3.0.0: 'SRR11947587/SRR11947587.sra' is a local non-kart file
2022-08-30T16:19:44 prefetch.3.0.0: 'SRR11947587/SRR11947587.sra' has 22 unresolved dependencies
2022-08-30T16:19:44 prefetch.3.0.0 int: connection unexpected while executing query within virtual file system module - cannot get remote location for 'NC_000067.6'

Lastly, from running fastq-dump on the downloaded sra file, I get the following

$ fastq-dump SRR11947587/SRR11947587.sra 
2022-08-30T16:20:56 fastq-dump.3.0.0 warn: connection unexpected while executing query within virtual file system module - can't open NC_000067.6 as a RefSeq or as a WGS
2022-08-30T16:20:56 fastq-dump.3.0.0 err: connection unexpected while executing query within virtual file system module - failed SRR11947587/SRR11947587.sra

=============================================================
An error occurred during processing.
A report was generated into the file '/home/mcuoco/ncbi_error_report.txt'.
If the problem persists, you may consider sending the file
to 'sra-tools@ncbi.nlm.nih.gov' for assistance.
=============================================================

fastq-dump quit with error code 3

Notably I have the same errors with sra-tools 2.11.0. Do you have any suggestions on how I can proceed here?

[klymenko]

What is the output of the following? curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=NC_000067.6

[mikecuoco]

$ curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=NC_000067.6
{
    "version": "2",
    "result": [
        {
            "bundle": "NC_000067.6",
            "status": 200,
            "msg": "ok",
            "files": [
                {
                    "object": "refseq|NC_000067.6",
                    "accession": "NC_000067.6",
                    "type": "sra",
                    "name": "NC_000067.6",
                    "size": 48187713,
                    "md5": "83ace9a2da16f7fbe5672c00d002ec9d",
                    "modificationDate": "2018-02-22T18:21:57Z",
                    "locations": [
                        {
                            "service": "sra-ncbi",
                            "region": "public",
                            "link": "https://sra-download.ncbi.nlm.nih.gov/traces/refseq/NC_000067.6"
                        }
                    ]
                }
            ]
        }
    ]
}

[mikecuoco]

Hi @klymenko I just want to follow-up here. Do you have any suspicions about what might be happening here?

[SJWScience]

Hi @mikecuoco, not sure if you are still having this issue. I had the exact same issue on our server. Interestingly I installed sra-tools on my local mac and was able to get the NC_XXXX file without issue (executing the same code as I had been previously), and then fasterq-dump worked without issue too. Where this might help you is that I was also able to copy that NC_XXXX file and put it in the same directory as the .sra files I was having the issue with on our server and after that fasterq-dump worked perfectly.

Doesn't solve whatever problem was causing it, but can certainly circumvent it.

[klymenko]

@mikecuoco, do you still have this issue?