-
Over the past 24 hours, I've tried using prefetch with multiple .krt files from multiple dbGaP projects, with no success. The input and output are always of the form:
`$ .../sratoolkit.3.1.1-centos…
-
When running prefetch on a particular dataset I'm seeing a message about 'unresolved dependencies':
And then when I try fasterq-dump on the prefetched dataset I get the following error:
Any …
-
### Problem Description
@jmtsuji This code fails.
```markdown
# For the long read data, to get the quality scores (i.e., not SRA Lite format), you will need to use the SRA Toolkit
# availab…
-
Extrapolated from common sequencing targets from the SRA, and sequences that returned false positives during initial database screenings:
- Human genome - integration sites: https://hgdownload.soe.…
-
SRX2591179 = Montipora capitata Spawning-Time1800_colony1
SRX2611210 = Montipora capitata Spawning-Time1800_colony10
-
### Description of the bug
I have a list of SRR IDs in a file and am trying to download them using the pipeline. However, I constantly get an error at the SRATOOLS_FASTERQDUMP step.
This is an exa…
-
Hello,
I'm encountering an issue with the NCBI SRA Toolkit, specifically with the `prefetch` command. I have been attempting to download data from the SRA database, but I keep running into SSL cert…
-
@Marlies1993 was running a distiller with some SRA-s as an input and the pipeline kept crashing at the sra step...
After closer inspection it appears that some of the links of this form: https://gith…
-
Hello how are you!
I'm trying to use the NCBI Magic-BLAST tool RNA-seq mapping tool, but I'm not getting it.
I followed the tutorial available on NCBI (https://ncbi.github.io/magicblast/cook/sra…
-
The current implementation of fastq-dl doesn't seem very robust to avoid downloading SRA-Lite files. One alternative is to reimplement the workflow by leveraging NCBI's Fasterq-dump directly