Cenote-taker 2 github
WebHi, I am struggling to find where the taxonomic classification is output. The CONTIG_SUMMARY has an ORGANISM_NAME, but no taxonomy. Is one meant to trace the ORGANISM_NAME to the database to find t... WebCenote-Taker2/unlimited_breadsticks.py at master · mtisza1/Cenote-Taker2 · GitHub mtisza1 / Cenote-Taker2 Public master Cenote-Taker2/unlimited_breadsticks.py / Jump to Go to file Cannot retrieve contributors at this time 82 lines (61 sloc) 5.72 KB Raw Blame #!/usr/bin/env python import argparse import sys, os import subprocess def str2bool ( v ):
Cenote-taker 2 github
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WebHi Mike, Thank you for Cenote-Taker2! However, I am facing a problem when i run the commond: This is my code: python /media/home/user05/anaconda3/envs/cenote-taker2 ... WebMar 26, 2024 · The download of the databases is not part of the conda recipe, and it is not common practice to do that mostly because of their size, so the download of the databases for cenote-taker2 is in the download-db.sh script the user needs to …
WebHello! Thank you for sharing this powerful tool. We just got Cenote-Taker2 installed in the system. I tried to run it using the test dataset "testcontigs_DNA_ct2.fasta" but always got a p... WebHi Jon, Thanks for opening this issue. Based on your problem, I'm going to guess you are trying to install this on a Mac. Unfortunately, I'm only able to support this tool on Linux machines, and the installation (including conda environment) only works on Linux.
WebJun 10, 2024 · I've had this happen on several other samples - at one point I ran about 10k Cenote-Taker2 runs, I'd say it happened in about 1-5% of samples. I saw another issue about this from months ago, but the fix was just to update to the latest version. I did a complete re-install of Cenote-Taker2 and still have the same issue. I've attached the log ... WebSep 13, 2024 · Run time with 7,000 viral genomes · Issue #14 · mtisza1/Cenote-Taker2 · GitHub Hello, I have been attempting to analyse a block of metagenomically derived putative viral genomes. These have been curated to a certain extent, so the confidence in the set is reaonably good. That said, I gave this job to a physical mac...
WebThe Unlimited Breadsticks module is included in the Cenote-Taker 2 repo, so no need to install it if you already have Cenote-Taker 2 (you may need to update cd Cenote-Taker2 …
WebDec 20, 2024 · cenote-taker2 vs (blastn nt & diamond nr) · Issue #42 · mtisza1/Cenote-Taker2 · GitHub Hi Mike, Recently， I ran cenote-taker2 and blastn against nt database & diamond against nr database with the contigs assembled by Megahit. I found that about 10000 sequences were classified as viruses, while about 1000 were identified by... in this moment concert 2022WebJan 25, 2024 · Sergey, Sorry again for the delay in replying. I'm glad you were able to get Unlimited Breadsticks to run. Your issue with rm and "Argument list too long" is not a fatal issue, but may result in having some intermediate files left over at the end. A user in a previous issue was able to find a solution #21, though I of course urge caution when … new job insurance doesn\u0027t kick in for 30 daysWebJun 3, 2024 · While Cenote-Taker 2 does take steps to earmark potential plasmids and conjugative transposons, extra precautions were taken by removing ∼4,000 putative viral sequences from the nonredundant database that contained replication-associated but not virion- or genome-packaging hallmark genes. in this moment clone heroWebSep 15, 2024 · Cenote-Taker2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. in this moment by karen kingsburyWebCenote-Taker 2 Version 2.1.2. If you haven't already installed Cenote-Taker 2, please follow installation instructions in README. If you have already installed it, please do: conda activate cenote-taker2_env conda … new job in peshawarWebYou should only click on links or attachments if you are certain that the email is genuine and the content is safe. Hey Darren, I have added an option --wrap which you can set to False in order to get sequences that are not clipped or rotated. You'll have to update Cenote-Taker 2 to v2.1.5 per the instructions. new job in assamWebOct 1, 2024 · Circularity detection and BlastN · Issue #15 · mtisza1/Cenote-Taker2 · GitHub Hello Mike, I'm using Cenote-Taker2 to discover viral elements in my samples. I'm really glad that there are lots of viral genes are identified but I have two questions and hope to have you suggestions. The end_feature of some metagenomi... in this moment concert