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Halting scg search with diamond v.09.26 #48
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Running on MacOS Mojave v10.14.6 |
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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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?
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