...
| Code Block |
|---|
kraken2 -db ~/SupportingData/kraken2/k2_pluspfp_20210127 \ --threads 32 \ Starter_examples-246915672/SMS2_S2_L001_R1_001.fastq.gz Starter_examples-246915672/SMS2_S2_L001_R2_001.fastq.gz \ --use-names --minimum-base-quality 25 --confidence 0.5 \ --report 05SMS2ReportConf25.txt --output xxx.txt |
Issues
rsync vs ftp
Under the hood, kraken2 uses rsync to download data. During testing we have experienced various issues while downloading databases.
For example:
| Code Block |
|---|
rsync: failed to connect to ftp.ncbi.nlm.nih.gov (130.14.250.10): Connection refused (111)
rsync: failed to connect to ftp.ncbi.nlm.nih.gov (130.14.250.12): Connection refused (111)
rsync: failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41f:250::229): Network is unreachable (101)
rsync: failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250::11): Network is unreachable (101)
rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.3] |
There are various issue pages discussing the problem (such as here), with the suggestion to use the --use-ftp option within the. See kraken2-build --help for further details.