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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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rna sqmtools erro #793

Closed Panda-smile closed 4 months ago

Panda-smile commented 4 months ago
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hello， jtamames ~ After running squeezemeta successfully ends, when using sqmtools to load data() for analysis, it is not recognized.

syslog.txt

fpusan commented 4 months ago

This seems correct. There are no binning results (you can't get bins from metatranscriptomic data) but this is just a warning. The data should be loaded correctly.

Panda-smile commented 4 months ago
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ERRO as data(), Unable to continue analysis

fpusan commented 4 months ago

Don't know what you mean with this screenshot. But summary(metatrans) should show that your project was loaded correctly.

Panda-smile commented 4 months ago
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I want to refer to this step for analysis, but the data() data cannot be loaded correctly, causing subsequent analysis to fail.

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Panda-smile commented 4 months ago
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now i stay at /mnt/hpc/home/zhanglj/Squeezemeta_20240108/FQ1toDJ，project name is： allshotgun This has the same problem as the sqmtools analysis of RNA just now，wish for professor reply~ thanks a lot~

fpusan commented 4 months ago

The data command is used to load our example data, but you don't need it since you have your own data (loaded under the variable name shotgun according to your screenshot above). Your idea was right but there is a typo in your code: shotgun.carb == subsetFun(shotgun, "Carbohydrate metabolism") You used the == operator (tests for equality) rather than = (used to assign variables). So it should be shotgun.carb = subsetFun(shotgun, "Carbohydrate metabolism")

Panda-smile commented 4 months ago

Thank you very much for the professor's answer. The problem has been solved~