User: tobias.v

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tobias.v0
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Posts by tobias.v

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EggNOG 4.5 database
... Can someone explain me why there are two eggNOG 4.5 databases for Bacteria? There is the precomputed HMM database for bactNOG and bact_50 available here: http://eggnogdb.embl.de/download/eggnog_4.5/hmmdb_levels/ ...
eggnog hmm written 9 weeks ago by tobias.v0 • updated 9 weeks ago by jhc2.5k
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Comment: C: local blast: makeblastdb: Abort trap 6
... I found out that formatdb is superseded by the makeblastdb command ...
written 4 months ago by tobias.v0
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Comment: C: local blast: makeblastdb: Abort trap 6
... next problem: formatdb command is not found... ...
written 4 months ago by tobias.v0
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Comment: C: local blast: makeblastdb: Abort trap 6
... yes it is unformatted text, also when I display invisible characters, the only invisible character is the new line feed. I did not try uppercase, because makeblastdb with lowercase letters has already worked ---edit--- I found out that I only get that Abort trap: 6 error when I add the flag -parse_ ...
written 4 months ago by tobias.v0
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Comment: C: local blast: makeblastdb: Abort trap 6
... I had an excel sheet with 3 columns: consecutive number, name of gene, sequence therefore I copied everything into a text editor and replaced all tabs with underscore, all slashes/colons with underscore etc and added a bigger than sign to the beginning, so this: >1.gene atgttgcaagagaaagt ...
written 4 months ago by tobias.v0 • updated 4 months ago by genomax32k
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Comment: A: local blast: makeblastdb: Abort trap 6
... makeblastdb -in Cat19_prot.fasta -parse_seqids -dbtype prot ...
written 4 months ago by tobias.v0
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local blast: makeblastdb: Abort trap 6
... I am running a standalone Blast 2.6.0 on my Mac OS 10.12.2 with 1.6 Ghz intel core i5 8 GB 1600 MHz DDR3. Everytime when I want to build a blast database with the makeblastdb command, I get the following error: Building a new DB, current time: 01/24/2017 09:13:26 New DB name: /Users/***/bin/blas ...
fasta makeblastdb blast written 4 months ago by tobias.v0
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Answer: A: Tool for calculating sequence statistic values (e.g. N50) for multiple bins
... perfect! format=5 did the trick for me thanks! ...
written 6 months ago by tobias.v0
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Tool for calculating sequence statistic values (e.g. N50) for multiple bins
... Does someone know a script to calculate sequence statistics such as N50, number of contigs, contigs length etc for multiple bins? So far, the genome tools seqstat script only calculates this for one bin. ...
assembly binning statistics written 6 months ago by tobias.v0

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