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chloroExtractorTeam / chloroExtractor

MIT License
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Blasterror in fcq. #132

Open Joyvalley opened 5 years ago

Joyvalley commented 5 years ago

Out of 17 assemblys CE got to this step 4 times. 12 died with the following error message: [scr] Failed to align minimum amount of reads (10000) to reference clusters 3 of the 4 that reached that step succeded, but one died with the following error message:

[19-04-14 16:58:23] [PipeWrap] Running 'fcg': /opt/chloroExtractor/bin/find_cyclic_graph.pl --in ass/assembly_graph.fastg --blastdb /opt/chloroExtractor/bin//../data/cds.nr98.fa --out fcg.fa
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = "en_IE:en",
        LC_ALL = (unset),
        LANG = "en_DK.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
[19-04-14 16:58:23] [fcg] Found 100 different nodes with 41455 bp total sequence length and 6 digraph information packages
[19-04-14 16:58:23] [fcg] Found 6 weakly connected components
[Sun Apr 14 16:58:23 2019] WCC:   0%
[Sun Apr 14 16:58:23 2019] WCC:   0%
[Sun Apr 14 16:58:23 2019] WCC:  16%
[Sun Apr 14 16:58:23 2019] WCC:  33%
[Sun Apr 14 16:58:23 2019] WCC:  50%
[Sun Apr 14 16:58:23 2019] WCC:  66%
[Sun Apr 14 16:58:23 2019] WCC:  83%
[Sun Apr 14 16:58:23 2019] WCC: 100%
[19-04-14 16:58:23] [fcg] No single circular chloroplast was found. Searching for partial hits...
Warning: [tblastx] Query is Empty!
[19-04-14 16:58:23] [fcg] Found 0 partial chloroplast sequences
greatfireball commented 5 years ago

Can you provide the name to the input file? @Joyvalley