If you are getting an error code 3 while running fasterq-dump, you have a few options. One of them is that the fasterq-dump has run out of memory. You can try to run fasterq-dump on another node, such as a compute node, but it may still not work.
Before you begin using fasterq-dump, make sure you have a working SRA-accessions file on your computer. SRA-accesses are the files that your fastq-dump program uses to load and write your fastq-dump files. The SRA-accesses file contains information about your samples and should be in the same directory as the fastq-dump files.
SRA-accessions provide an easy way to download all SRA-related documents from SRA. The utility will download the files to your current working directory and rename them to match their locality or materialSampleID. You can also choose to download the files directly to your computer using the fastq-dump utility.
FASTQ-Dump is a command-line tool for downloading sequence reads from SRA. It can take a lot of disk space. But the utility uses temporary files and multi-threading to speed up the process. The minimum space required for FASTQ-dump to run is 1MB. It is a part of the Genome Analysis Toolkit 4 from the Broad institute.
After the fastq tool has finished downloading the data, it analyzes the raw data. This tool also creates separate collections for different types of data. Besides sequencing files, it can also store the raw data for each SRA-accessions run.
Downloads data in FASTQ format
The SeqSphere+ software allows you to download FASTQ files from the NCBI Sequence Read Archive, also known as SRA. Once you have downloaded the FASTQ file, you can analyze it with the help of different tools. However, you should note that before you process the FASTQ files, you should prepare them for analysis. In order to do this, you need to export their metadata into MS Excel.
Once you have the raw data in FASTQ format, you can begin processing it with the SeqSphere+ Pipeline. To do this, first download the SRA file using direct https. Once this is complete, SeqSphere+ will convert the file to FASTQ by using the SRA toolkit. Note that this method is slightly slower than the direct download, but the resulting FASTQ file is ready for analysis.
Renames files based on locality
Fasterq-dump is a tool that renames files based on local location. It downloads documents to your current working directory and renames them based on their locality. It uses the materialSampleID to determine the locality of files. It also saves the temporary files in /ncbi/public/sra. You can run fasterq-dump on any Helix node, but this may not work if you are using a compute node.
FASTQ-dump works with SRA-accessions, which are created with the NCBI Sequence Read Archive Toolkit. These SRA-accessions contain a library accession, an experiment accession, and a run accession. Each of these elements represents the metadata associated with a study. The run accession represents the sequencing experiment data. FASTQ-dump requires an SRA toolkit version 2.10.8 or higher to work properly. FASTQ-dump downloads data in either FASP or https modes.
Renames files based on materialSampleID
The fastq-dump tool is a tool that downloads documents into your current working directory and renames them based on their materialSampleID. It then saves the files to /ncbi/public/sra. If you are not using the compute node, you may want to run this tool on Helix.