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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Document "output_directory/logs/err" write "Error: Incomplete database file. Database building did not complete successfully". #67

Open xdli009 opened 4 years ago

xdli009 commented 4 years ago

Hello, Simroux Document "output_directory/logs/err" write "Error: Incomplete database file. Database building did not complete successfully".But the file "virsorter-data-v2.tar.gz" that is downloaded by me is complete,and md5sum returned dd12af7d13da0a85df0a9106e9346b45.Furthermore, the result file "VIRSorter_global-phage-signal.csv" has 3625 lines. I was wondering how to solve this problem.

Command Input: wrapper_phage_contigs_sorter_iPlant.pl -f ${fa_dir}/final.contigs.fa --db 1 --wdir ${output_dir} --data-dir ${data_dir}/virsorter-data --ncpu 20 --diamond

Thanks a lot, hope to get your suggestions!

simroux commented 4 years ago

Hi, Could you paste or enclose the out and err files here ? It looks to me as an error in the step where VirSorter tries to use the results from the first round of detection to (maybe) refine borderline calls, but this is not a required step, so most likely the results you have (in "VIRSorter_global-phage-signal.csv") are correct.

xdli009 commented 4 years ago

err.txt File “output_directory/logs/out” size is 1.45GB,so it cannot be uploaded.The content at the end of the file is as follows. We had checked VIRSorter_k141_10000171_flag=1_multi=1_0000_len=661 -> VIRSorter_k141_10000171_flag=1_multi=1_0000_len=661 .. predicted to be a complete phage.. We had checked VIRSorter_k141_1904711_flag=1_multi=2_0000_len=659 -> VIRSorter_k141_1904711_flag=1_multi=2_0000_len=659 .. predicted to be a complete phage.. We had checked VIRSorter_k141_6946272_flag=0_multi=1_0000_len=644 -> VIRSorter_k141_6946272_flag=0_multi=1_0000_len=644 .. predicted to be a complete phage.. We had checked VIRSorter_k141_4460294_flag=1_multi=1_0000_len=639 -> VIRSorter_k141_4460294_flag=1_multi=1_0000_len=639 .. predicted to be a complete phage.. We had checked VIRSorter_k141_5558572_flag=1_multi=1_0000_len=623 -> VIRSorter_k141_5558572_flag=1_multi=1_0000_len=623 .. predicted to be a complete phage.. We had checked VIRSorter_k141_6122220_flag=0_multi=1_0000_len=587 -> VIRSorter_k141_6122220_flag=0_multi=1_0000_len=587 .. predicted to be a complete phage.. We had checked VIRSorter_k141_4352118_flag=1_multi=3_0000_len=568 -> VIRSorter_k141_4352118_flag=1_multi=3_0000_len=568 .. predicted to be a complete phage.. We had checked VIRSorter_k141_5790063_flag=1_multi=2_0000_len=566 -> VIRSorter_k141_5790063_flag=1_multi=2_0000_len=566 .. predicted to be a complete phage.. We had checked VIRSorter_k141_7328126_flag=0_multi=1_0000_len=566 -> VIRSorter_k141_7328126_flag=0_multi=1_0000_len=566 .. predicted to be a complete phage.. We had checked VIRSorter_k141_3387844_flag=1_multi=1_0000_len=543 -> VIRSorter_k141_3387844_flag=1_multi=1_0000_len=543 .. predicted to be a complete phage.. We had checked VIRSorter_k141_3652285_flag=1_multi=2_0000_len=533 -> VIRSorter_k141_3652285_flag=1_multi=2_0000_len=533 .. predicted to be a complete phage.. We had checked VIRSorter_k141_4725713_flag=1_multi=2_0000_len=468 -> VIRSorter_k141_4725713_flag=1_multi=2_0000_len=468 .. predicted to be a complete phage.. We had checked VIRSorter_k141_251206_flag=1_multi=3_0000_len=402 -> VIRSorter_k141_251206_flag=1_multi=3_0000_len=402 .. predicted to be a complete phage.. (END)

simroux commented 4 years ago

Ok, so it looks like VirSorter indeed completed successfully, and you should be able to work with the results you got. Let me know if ever you see anything weird in the predictions.