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Halting scg search with diamond v.09.26 #48

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DeepSea-Stokke opened this issue Nov 7, 2019 · 2 comments
Open

Halting scg search with diamond v.09.26 #48

DeepSea-Stokke opened this issue Nov 7, 2019 · 2 comments

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@DeepSea-Stokke
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Hi,
I have just upgraded to DAS_TooL v1.1.2 which halts with following error message for both my data and test data:

DAS_Tool-master nimst$ ./DAS_Tool -i sample_data/sample.human.gut_concoct_scaffolds2bin.tsv,sample_data/sample.human.gut_maxbin2_scaffolds2bin.tsv,sample_data/sample.human.gut_metabat_scaffolds2bin.tsv,sample_data/sample.human.gut_tetraESOM_scaffolds2bin.tsv -l concoct,maxbin,metabat,tetraESOM -c sample_data/sample.human.gut_contigs.fa -o sample_test/DASToolRun1 --search_engine diamond
diamond v0.9.26.127 | by Benjamin Buchfink [email protected]
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

Running DAS Tool using 1 threads.
predicting genes using Prodigal V2.6.3: February, 2016
diamond v0.9.26.127 | by Benjamin Buchfink [email protected]
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

identifying single copy genes using diamond version 0.9.26
mv: cannot stat 'sample_test/DASToolRun1_proteins.faa.scg': No such file or directory
mv: cannot stat 'sample_test/DASToolRun1_proteins.faa.scg': No such file or directory
rm: cannot remove 'sample_test/DASToolRun1_proteins.faa.scg.candidates.faa': No such file or directory
rm: cannot remove 'sample_test/DASToolRun1_proteins.faa.all.b6': No such file or directory

After debugging it seems as if the issue was diamond itself (v0.9.26.127):
Searching alignments... blast did not work, please check your input file.
single copy gene prediction using diamond failed. Aborting

Downgrading to latest working diamond version (v0.9.22) with DAS_TooL 1.1.0 solved the problem and DAS_TooL runs smoothly. Do you know if there are any known issues with the latest version of diamond that would affect DAS_TooL v.1.1.2?

@DeepSea-Stokke
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Running on MacOS Mojave v10.14.6

@cmks
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cmks commented Nov 8, 2019

I've tested the latest version of DAS Tool with Diamond v0.9.26 and didn't encounter any issues. Also, DAS Tool 1.1.1 should be able to run with Diamond 0.9.26.

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