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From: Douglas Duane Rhoads
Subject: Error
Date: Wed, 2 Nov 2022 21:11:59 +0000

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/ -d "genbank" -T "1280" -c ""

-l "" -f "genomic.fna.gz, assembly_report.txt" -o "Saureus" -t 12 -r


┌─┐┌─┐┌┐┌┌─┐┌┬┐┌─┐    ┬ ┬┌─┐┌┬┐┌─┐┌┬┐┌─┐┬─┐

│ ┬├┤ ││││ ││││├┤     │ │├─┘ ││├─┤ │ ├┤ ├┬┘

└─┘└─┘┘└┘└─┘┴ ┴└─┘────└─┘┴  ─┴┘┴ ┴ ┴ └─┘┴└─



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 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


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