jellyfish: No such file or directory

[sum732]

Hello,

I just downloaded and build from git: /Kraken/KrakenUniq/krakenuniq-0.7.3/krakenuniq-build --version KrakenUniq version 0.7.3 Copyright 2017-2018, Florian Breitwieser (fbreitwieser@jhu.edu) Copyright 2013-2017, Derrick Wood (dwood@cs.jhu.edu) for Kraken

I am seeing the following error:

Kraken build set to minimize RAM usage.
Found 8 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory.
Creating k-mer set (step 1 of 6)...
Using /Kraken/KrakenUniq/krakenuniq-0.7.3/jellyfish-install/bin/jellyfish
Hash size not specified, using '42980199277'
/Kraken/KrakenUniq/krakenuniq-0.7.3/build_db.sh: line 46: /Kraken/KrakenUniq/krakenuniq-0.7. 3/jellyfish-install/bin/jellyfish: No such file or directory xargs: cat: terminated by signal 13

I even tried with conda and still seeing the exact same error.

Any help will be greatly appreciated. Many Thanks, Deep

[alekseyzimin]

Please make sure you run install_krakenuniq with -j option if you need to build databases.

[douglasgscofield]

In the past we have relied upon a separate installation of jellyfish when installing KrakenUniq. This appears no longer to be possible?

[salzberg]

In the past we have relied upon a separate installation of jellyfish when installing KrakenUniq. This appears no longer to be possible?

it should still be possible. We include jellyfish in the package because KrakenUniq uses an older release of jellyfish - so if you use your own (up-to-date) version, then KrakenUniq won't work. The newer releases of jellyfish aren't backward-compatible.

[douglasgscofield]

We ended up with the same error as above, but with 1.0.1, though we built KrakenUniq/1.0.1 with jellyfish/1.1.12 loaded. We didn't build with install_krakenuniq.sh -j, assuming that jellyfish/1.1.12 sufficed.

/sw/bioinfo/KrakenUniq/1.0.1/rackham/build_db.sh: line 46: /sw/bioinfo/KrakenUniq/1.0.1/rackham/jellyfish-install/bin/jellyfish: No such file or directory

Now I see that build_db.sh will use $JELLYFISH_BIN for its jellyfish executable if that is not empty, otherwise it will use the tree-local version. $JELLYFISH_BIN is defined by krakenuniq-build at line 199 based on the value of the --jellyfish-bin= option, but this overwrites (the local version of) the environment variable with an empty string if that option was not provided, which means that, e.g., I can't define $JELLYFISH_BIN external to KrakenUniq and have it use that as its jellyfish, and it seems the tool also no longer uses check_for_jellyfish.sh to find a jellyfish 1 in its PATH.

It's not a problem to use the jellyfish 1 from the KrakenUniq tree, and we'll do that from now on, but it seems the ability to use a jellyfish 1 from the PATH has been lost somewhere along the way.

[alekseyzimin]

I have just updated the code to prevent overwriting $JELLYFISH_BIN variable when option --jellyfish-bin= is not supplied. Please git pull the latest changes, there is only one line changed in krakenuniq-build.

[sepidehalamouti]

Hi Alekseyzimin I have a similar problem with jellyfish with the latest version of KrakenUniqu installed using Conda: This is the error I get for the build: /miniconda3/libexec/build_db.sh: line 64: JELLYFISH_BIN: unbound variable

[alekseyzimin]

What is the version installed with Conda?

On Tue, Mar 14, 2023 at 4:29 PM sepidehalamouti @.***> wrote:

Hi Alekseyzimin I have a similar problem with jellyfish with the latest version of KrakenUniqu installed using Conda: This is the error I get for the build: /shared/home/salamouti/miniconda3/libexec/build_db.sh: line 64: JELLYFISH_BIN: unbound variable

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[sepidehalamouti]

Hi Alekseyzimin, I have version 1.0.3 installed with Conda. I resolved the first error with --jellyfish-bin option but now I have a cat error as follow: cat: library/bacteria/Complete_Genome/Chordicoccus_furentiruminis_stra: No such file or directory

The directory contains the .fna and .map files of that species: ls library/bacteria/Complete_Genome/Chordicoccus_furentiruminis_stra* library/bacteria/Complete_Genome/Chordicoccus_furentiruminis_strain_MP1D12-tax2709410-GCF_019355395.1_ASM1935539v1_genomic-dustmasked.fna library/bacteria/Complete_Genome/Chordicoccus_furentiruminis_strain_MP1D12-tax2709410-GCF_019355395.1_ASM1935539v1_genomic.fna.map

Thank you