Created
April 7, 2020 09:23
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| ./metaeuk/bin/metaeuk easy-predict GCF_000709125.1_Exop_aqua_CBS_119918_V1_genomic.fna \ | |
| 2020_TAX_DB \ | |
| results.fasta \ | |
| tmp \ | |
| --threads 1 \ | |
| --slice-search | |
| Tmp tmp folder does not exist or is not a directory. | |
| Create dir tmp | |
| easy-predict GCF_000709125.1_Exop_aqua_CBS_119918_V1_genomic.fna 2020_TAX_DB results.fasta tmp --threads 1 --slice-search | |
| MMseqs Version: ddf27427fd65b7763bdde3787e9a9b4a8ec27371 | |
| Substitution matrix nucl:nucleotide.out,aa:blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| Allow wrapped scoring false | |
| E-value threshold 100 | |
| Seq. id. threshold 0 | |
| Min alignment length 0 | |
| Seq. id. mode 0 | |
| Alternative alignments 0 | |
| Coverage threshold 0 | |
| Coverage mode 0 | |
| Max sequence length 65535 | |
| Compositional bias 1 | |
| Realign hits false | |
| Max reject 2147483647 | |
| Max accept 2147483647 | |
| Include identical seq. id. false | |
| Preload mode 0 | |
| Pseudo count a 1 | |
| Pseudo count b 1.5 | |
| Score bias 0 | |
| Gap open cost 11 | |
| Gap extension cost 1 | |
| Zdrop 40 | |
| Threads 1 | |
| Compressed 0 | |
| Verbosity 3 | |
| Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out | |
| Sensitivity 4 | |
| k-mer length 0 | |
| k-score 2147483647 | |
| Alphabet size nucl:5,aa:21 | |
| Max results per query 300 | |
| Split database 0 | |
| Split mode 2 | |
| Split memory limit 0 | |
| Diagonal scoring true | |
| Exact k-mer matching 0 | |
| Mask residues 1 | |
| Mask lower case residues 0 | |
| Minimum diagonal score 15 | |
| Spaced k-mers 1 | |
| paced k-mer pattern | |
| Local temporary path | |
| Rescore mode 0 | |
| Remove hits by seq. id. and coverage false | |
| Sort results 0 | |
| Mask profile 1 | |
| Profile e-value threshold 0.001 | |
| Global sequence weighting false | |
| Allow deletions false | |
| Filter MSA 1 | |
| Maximum seq. id. threshold 0.9 | |
| Minimum seq. id. 0 | |
| Minimum score per column -20 | |
| Minimum coverage 0 | |
| Select N most diverse seqs 1000 | |
| Omit consensus false | |
| Min codons in orf 15 | |
| Max codons in length 32734 | |
| Max orf gaps 2147483647 | |
| Contig start mode 2 | |
| Contig end mode 2 | |
| Orf start mode 1 | |
| Forward frames 1,2,3 | |
| Reverse frames 1,2,3 | |
| Translation table 1 | |
| Translate orf 0 | |
| Use all table starts false | |
| Offset of numeric ids 0 | |
| Create lookup 0 | |
| Add orf stop false | |
| Chain overlapping alignments 0 | |
| Merge query 1 | |
| Search type 0 | |
| Search iterations 1 | |
| Start sensitivity 4 | |
| Search steps 1 | |
| Slice search mode true | |
| Strand selection 1 | |
| Disk space limit 0 | |
| MPI runner | |
| Force restart with latest tmp false | |
| Remove temporary files false | |
| maximal combined evalue of an optimal set 0.001 | |
| minimal length ratio between combined optimal set and target 0.5 | |
| Maximal intron length 10000 | |
| Minimal intron length 15 | |
| Minimal exon length aa 11 | |
| Maximal overlap of exons 10 | |
| Gap open penalty -1 | |
| Gap extend penalty -1 | |
| allow same-strand overlaps 0 | |
| translate codons to AAs 0 | |
| write target key instead of accession 0 | |
| Reverse AA Fragments 0 | |
| createdb GCF_000709125.1_Exop_aqua_CBS_119918_V1_genomic.fna tmp/6584864355691299934/contigs --dbtype 2 --compressed 0 -v 3 | |
| Converting sequences | |
| [102] 0s 349ms | |
| Time for merging to contigs_h: 0h 0m 0s 257ms | |
| Time for merging to contigs: 0h 0m 0s 736ms | |
| Database type: Nucleotide | |
| Time for merging to contigs.lookup: 0h 0m 0s 5ms | |
| Time for processing: 0h 0m 4s 817ms | |
| createdb 2020_TAX_DB tmp/6584864355691299934/targets --dbtype 1 --compressed 0 -v 3 | |
| Converting sequences | |
| Fasta entry: 0 is invalid. | |
| Error: targets createdb died |
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