Not certain what is happening but this command has been working for a year or more in WSL2Ubuntu on a Win 11-64bit machine (fully updated). I just did a sudo apt upgrade when I started this time and several packages were updated. The
screen output is as follows, and I was not using the -p switch for parallel.
(base) dougrhoads@ARSC-A-G4LJXP3:/mnt/f/DNAwork/Saureus$ $HOME/tools/genome_updater/genome_updater.sh -d "genbank" -T "1280" -c ""
-l "" -f "genomic.fna.gz, assembly_report.txt" -o "Saureus" -t 12 -r
-------------------------------------------
┌─┐┌─┐┌┐┌┌─┐┌┬┐┌─┐ ┬ ┬┌─┐┌┬┐┌─┐┌┬┐┌─┐┬─┐
│ ┬├┤ ││││ ││││├┤ │ │├─┘ ││├─┤ │ ├┤ ├┬┘
└─┘└─┘┘└┘└─┘┴ ┴└─┘────└─┘┴ ─┴┘┴ ┴ ┴ └─┘┴└─
v0.5.1
-------------------------------------------
Mode: NEW
Args: -T '1280' -t '12' -o 'Saureus' -f 'genomic.fna.gz, assembly_report.txt' -d 'genbank' -r
Outp: /mnt/f/DNAwork/Saureus/Saureus/
-------------------------------------
Downloading assembly summary [2022-11-02_16-00-33]
- Database [genbank]
- 1432513 assembly entries available
Filtering assembly summary [2022-11-02_16-00-33]
- Downloading taxonomy (ncbi)
- 1401213 assemblies removed not in taxids [1280]
- 31300 assembly entries to download
Downloading 62600 files with 12 threads
parallel: This should not happen. You have found a bug.
Please contact
parallel@gnu.org and include:
* The version number: 20161222
* The bugid: Can't dup STDOUT: No such file or directory
* The command line being run
* The files being read (put the files on a webserver if they are big)
If you get the error on smaller/fewer files, please include those instead.
(base) dougrhoads@ARSC-A-G4LJXP3:/mnt/f/DNAwork/Saureus$
I can’t put the files on a server because they are on the NCBI server, and I can’t download them without genome_updater.sh??
