Daniel Malzl
Daniel Malzl
Ah I see. However, I wanted to leave this here for future references. Thanks anyway
didn't dare to try it yet as I did not want to break the cluster again and since IT very strongly suggested to not use it anymore. In anyway they...
so for me most of them still work just some are not available. did you try use teh `--force_sratools_download` option
Although I think fetchngs is designed to also link these back SRA accessions I would suggest using the SRA run selector or the Entrez API to link GSM to SRA...
Could you post the exact error you get and for which process this occurs?
Okay this is the same thing I get connected to this [issue](https://github.com/nf-core/fetchngs/issues/99). What I did to get around this is locally changing the [bin/sra_ids_to_runinfo.py](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) file so that the ENA FTP...
Hi @drpatelh, Unfortunately, the only things I could come up with is using the ENA FTP by default and falling back on the FTP when prefetch failed. So what I...
On the same issue, there seems to be a problem with configuration of the sra-toolkit as I get this message after resolving the command line parameter issue ``` This sra...
Ah sorry this is my fault. I had the configuration problem before and therefore used the preinstalled module I have on our cluster which is v2.9.6.1. Didn't anticipate the version...
Sorry for being annoying but I joined and don't find the fetchngs channel. Just have pipelines is this the one you were referring to?