prefetch not downloading phenotype files

[drmurdock]

Hi, I'm trying to download phenotype data files from dbGap using the prefetch tool but haven't had any success.

Command: /Users/dmurdock/Desktop/sratoolkit.3.0.1-mac64/bin/prefetch --ngc my_ngc_file.ngc my_cart_file.krt

Output: 2022-12-02T15:57:27 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T15:57:27 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T15:57:28 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T15:57:28 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T15:57:28 prefetch.3.0.1 int: buffer insufficient while converting string within text module - VPathReadUri(VResolverRemote): 2046999 2022-12-02T15:57:29 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T15:57:29 prefetch.3.0.1 int: buffer insufficient while converting string within text module - VPathReadUri(VResolverRemote): 2047002 2022-12-02T15:57:29 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T15:57:29 prefetch.3.0.1 int: buffer insufficient while converting string within text module - VPathReadUri(VResolverRemote): 2047005

Nothing is actually downloaded, however. I'm using the latest version of the SRA toolkit. It's only about 30 Kb of data so I'm not sure what's going on. I'm new to this tool but can't see anything obviously wrong with my command. I'd appreciate any insight. Thanks.

[klymenko]

Are you running on Mac?

[drmurdock]

Yes, MacOs 11.6.1. I've been trying to download 6 txt.gz files. After trial and error, I was able to download 3 of them individually, but I still get the same error with the other 3. Thanks.

2022-12-02T19:57:38 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T19:57:38 prefetch.3.0.1 int: buffer insufficient while converting string within text module - VPathReadUri(VResolverRemote): 2046999 2022-12-02T19:57:38 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T19:57:38 prefetch.3.0.1 int: buffer insufficient while converting string within text module - VPathReadUri(VResolverRemote): 2047002 2022-12-02T19:57:38 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-02T19:57:38 prefetch.3.0.1 int: buffer insufficient while converting string within text module - VPathReadUri(VResolverRemote): 2047005

[snu-mchoi]

Hi, I experienced a similar problem in Ubuntu. /some_path/sratoolkit.3.0.1-ubuntu64/bin/prefetch --ngc ./xxx.ngc ./cart_prjxxx.krt (For me, my sratools is installed in ssd drive, and I'm running my commands in synology drive)

It outputs multiple lines of "Current preference is set to retrieve SRA Normalized Format files with full base quality scores.". Everything seems fine but after all the process is done, nothing was downloaded.

2022-12-07T13:02:53 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:02:58 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:03:04 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:03:10 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:03:22 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:04:42 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:04:48 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-07T13:04:53 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.

Thanks !

[drmurdock]

Thanks @mchoistudent. Did you eventually figure out what the problem was? I still can't download the files.

[klymenko]

@drmurdock, it is a bug, we are preparing a new release. Meanwhile please try https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/dev/prefetch.3.0.2rc-mac64.tar.gz .

@mchoistudent, create a new issue.

[drmurdock]

Thank you @klymenko! I was able to download the files.

[Dzhan4]

Opening this back, I'm having the same problem trying to download phenotype files on Centos.

Tried with

./prefetch --ngc ../xxx.ngc ../yyy.krt

and with:

./prefetch.3.0.2 --ngc ../xxx.ngc ../yyy.krt

Same issue, getting following output with empty folders:

2023-01-25T22:37:11 prefetch.3.0.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-01-25T22:37:11 prefetch.3.0.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-01-25T22:37:12 prefetch.3.0.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-01-25T22:37:12 prefetch.3.0.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-01-25T22:37:13 prefetch.3.0.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-01-25T22:37:14 prefetch.3.0.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.