Question: Unknown argument '--ngc'
0
gravatar for mendonca_thiago22
5 weeks ago by
mendonca_thiago220 wrote:

Hey guys, I'm trying to download dbGap data from a cart file and I keep getting this error message, what could be a solution to it? Thanks!

/mnt/c/bio/sratoolkit.2.10.9-ubuntu64/bin$ prefetch --ngc /mnt/c/bio/prj_26363.ngc /mnt/c/bio/cart_DAR99004_202101251434.krt

2021-01-26T14:45:41 prefetch.2.8.2 err: libs/kapp/args.c:1262:ArgsParseInt: param unknown while parsing argument list within application support module - Unknown argument '--ngc'
2021-01-26T14:45:41 prefetch.2.8.2 int: libs/kapp/args.c:1262:ArgsParseInt: param unknown while parsing argument list within application support module - ArgsMakeAndHandle
ngc prefetch sra software error • 112 views
ADD COMMENTlink modified 5 weeks ago by rpolicastro3.9k • written 5 weeks ago by mendonca_thiago220
1
gravatar for ATpoint
5 weeks ago by
ATpoint46k
ATpoint46k wrote:

Could be a newer option, is your sratools version up-to-date?

ADD COMMENTlink written 5 weeks ago by ATpoint46k

I'm using the latest version

ADD REPLYlink written 5 weeks ago by mendonca_thiago220
1

No you arent't. You are in a folder with version 2.10.9 but the message says 2.8.2. If there is a binary you want to use in that bin folder do ./prefetch. Currently you are calling a binary that is somewhere in $PATH.

From being in the folder do ./prefetch --ngc /mnt/c/bio/prj_26363.ngc /mnt/c/bio/cart_DAR99004_202101251434.krt

ADD REPLYlink written 5 weeks ago by ATpoint46k

Oh right It worked! Thanks!

ADD REPLYlink written 5 weeks ago by mendonca_thiago220
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