User: shibl_a

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shibl_a20
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Posts by shibl_a

<prev • 14 results • page 1 of 2 • next >
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Kaiju or MetaPhlAn2?
... A question for those who have experience with metagenomic datasets...which of those two tools would you prefer to use with a metagenomic dataset derived from a seawater sample in terms of reliability and more accurate representation of the taxa..?? Thanks! ...
kaiju taxonomy metaphlan2 metagenomics written 5 months ago by shibl_a20
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Normalization to fit bars on GraPhlAn generated cladogram
... Hello, I recently generated a cladogram on GraPhlAn from my Metaphlan2 output and wanted to add a ring displaying the relative abundances of each clade. I created a text file with this information according to the example (https://bitbucket.org/nsegata/graphlan/src/default/examples/guide/annot_3.tx ...
normalization graphlan metaphlan2 cladogram written 6 months ago by shibl_a20 • updated 10 weeks ago by francesco.asnicar0
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HUMANn2 test error
... Installed humann2 recently on Ubuntu 16.04 Ran `humann2_test` and all was ok Ran `humann2_test --run-functional-tests-tools` and all was ok Ran `humann2_test --run-functional-tests-end-to-end` and got the following one error (below are the last few output lines of this command ...
humann2 functional analysis testing error written 7 months ago by shibl_a20 • updated 7 months ago by WouterDeCoster40k
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Comment: C: CheckM and pplacer error
... That was the first thing I tried but this is what the conda command returns Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - pplacer Current channels: - https://conda.anaconda.org/biocond ...
written 7 months ago by shibl_a20
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CheckM and pplacer error
... I installed checkm using bioconda and downloaded pplacer from its site. I then moved all the pplacer executables into the checkm bin. When I run this command: $ checkm lineage_wf --pplacer_threads 2 checkm_input checkm_output I get this output: ****************************************** ...
genome quality phylogeny bins checkm pplacer written 7 months ago by shibl_a20
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Answer: A: REALPHY and JAVA compatibility issue or not?
... Resolved (for now)...the problem was in the config.txt file ...
written 9 months ago by shibl_a20
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REALPHY and JAVA compatibility issue or not?
... I'm trying to use REALPHY to generate a phylogeny tree based on whole (bacterial) genomes. When I run the commands "REALPHY_V112 realphy_input realphy_output" or "java -jar RealPhy_v112.jar ~/Desktop/realphy_input ~/Desktop/realphy_output" I get the same error: Exception in thread "main" java.lang. ...
whole genome-based phylogeny java tree realphy written 9 months ago by shibl_a20
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Comment: C: Organizing tools/ software
... I like the idea of being able to have everything I need for a project in one place. I'll check out docker. Thanks for the inspiration. ...
written 9 months ago by shibl_a20
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Comment: C: Organizing tools/ software
... Thank you for your suggestion. It was the closest I could find to describe my question. If there were other tags I would've used them. ...
written 9 months ago by shibl_a20
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Organizing tools/ software
... I constantly download tools and programs to work with. I don't want to have to create a new PATH every time. How can I organize ALL my tools/ programs/ scripts (old and new) into one place so that I don't have to worry about running commands from anywhere on my terminal? any ideas? ...
software error written 9 months ago by shibl_a20 • updated 9 months ago by kloetzl1.0k

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