conterminator

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fail to predict inserted contamination

5

Hello! I did a synthetic genome to check the outputs and the conterminator failed to predict inserted contaminants. **Infos:** Version: 1.c74b5 Organisms in this synthetic genome: Saccharum hybrid cultivar SP80-3280,...

felipevzps

Error: kmermatcher step died

1

Hi @martin-steinegger, thanks for making conterminator available. I've been trying to run it on a 450 GB fasta file, using 20 CPUs and 450 GB of RAM, but keep getting...

gbdias

Hi, I am searching for contaminant sequences in a genome assembly (using the NT database) and am a bit confused about the values in the "Corrected contig length" column in...

casolp

Invalid pointer during calculation of alignments

1

Version: `commit 3eabfaff83bb77eac5ef342e8905cc4f7d378cb7` Command: ``` ./conterminator/build/bin/conterminator protein GTDB97.faa taxonomy/mapping_new conterminator_phylum_level conterminator_tmp --threads 64 --ncbi-tax-dump taxonomy --kingdoms 3,9,22,28,71,85,104,113,188,435,558,600,661,798,948,2112,2179,2185,2197,2222,2231,2290,2346,2367,2457,2526,2599,2662,2804,2844,2936,2947,3026,3093,3196,3236,3259,3295,3332,3478,3486,3519,3588,3721,3764,3806,3852,3869,3971,4049,4123,4138,4295,4380,4393,4426,4438,4480,4574,4637,4747,4807,4962,5058,5211,5295,5301,5341,5428,5455,5610,5785,5850,5876,6053,6077,6352,6994,7152,7497,7678,7997,8069,8163,8265,8415,8508,9033,9459,9518,9602,9620,9659,9816,9982,10092,10112,10373,10409,10624,10701,10941,10980,11478,12122,12426,12439,12474,12788,12916,13990,14290,14512,14627,14692,14712,14955,15712,16418,16488,17029,17211,17233,17428,17878,17918,18303,18551,19564,19757,19952,20114,20624,21463,22205,22539,22684,23843,24111,24497,26693,27254,29002,29170,30513,31392,32011,33650,34643,34865,35143 ``` Output: ``` Tmp conterminator_tmp folder does not exist or is not a...

apcamargo

List of accession numbers for contamination in NR

10

Thanks for addressing the contamination issue (again)! I am interested in cleaning up the NR database before using it for my application. Would it be possible to also make available...

pmenzel

pvanheus