prefetch fails downloading

[ebrigos]

I am trying to download genotype imputed data from an accepted project from dbGaP. Once the access has been granted, I've followed the download guidelines with the recommended configuration.

To download the files, I've used the combination of the kart file and my fresh dbGaP repository key:

$ prefetch --ngc prj_XXXXX.ngc cart_DAR116945_202212151302.krt

Even if it connects with the server and is able to find the correct file, this error rises:

Downloading kart file 'cart_DAR116945_202212151302.krt'
Checking sizes of kart files...
2023-01-16T13:24:42 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
Downloading the files...
2023-01-16T13:24:43 prefetch.3.0.1: 1) Downloading 'phg000130.v1.GENEVA_VenousThrombosis_imputed.genotype-imputed-data.chr21.c1.GRU.tar'...
2023-01-16T13:24:43 prefetch.3.0.1:  Downloading via HTTPS...
2023-01-16T13:25:35 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead

[klymenko]

email to sra@ncbi.nlm.nih.gov

[ebrigos]

Dear Andrew,

I have already emailed them and I have been waiting for an answer for more than two months... I would really need some help with this error because it is delaying an important step of the research project. I don't know what else to do to find any kind of assistance from SRA/NCBI.

Thanks,

Eva

Missatge de Andrew Klymenko @.***> del dia dc., 8 de març 2023 a les 16:36:

email to @.***

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[klymenko]

@ebrigos , send them your kart file and the number of dbGaP project. @stineaj , please ask curators to notify me when they receive this.

[klymenko]

@ebrigos, did you succeed?