phyloFlash
phyloFlash copied to clipboard
HRGV
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
Hi! Thanks for developing this tool! I'm getting a somewhat mysterious error that I'm hoping to get some help with! The error occurred on the following subcommand: ``` running subcommand:...
Hi! I'm trying to install Phyloflash on my macbook, but during the installation is not able to find the bedtools release in any of the conda channels. Suggestions?
I'm using "conda install phyloflash" to install phyloflash, and some errors are reported below: ``` Found conflicts! Looking for incompatible packages. failed UnsatisfiableError: The following specifications were found to be...
Thanks for developing such good software! I read the `Manual` carefully and found that there is no command line(eg. -o or --output) to save the results? What can I found...
Dear Phyloflash team, I want to install it but after following the protocol to install from conda (including the step with strict channel), it just take forever and never stop...
Hi, I have been trying to create a heatmap using phyloFlash_heatmap.R, but with the samples clustered by phylogeny. I have generated a distance matrix based on 18S, and am attempting...
I am currently trying to install phyloFlash in a brand new conda environment, however, it doesn't move past the "solving environment" stage. It hasn't moved past this stage of the...
Hi @HRGV and @kbseah , I have been using phyloFalsh to explore the eukaryotic component of some metagenomes and noticed that the taxonomic paths in the .phyloFlash.NTUfull_abundance.csv output table are...
The log: ``` This is phyloFlash v3.4.2 [20:33:07] Using dbhome '/workspaces/genome_assembly/tmp/work/25/0e1e09f4cc53ded5f987a83f5db393/PHYLOFLASH_DB' [20:33:07] working on library FINAL [20:33:07] Forward reads read1.fq [20:33:07] Reverse reads read2.fq [20:33:07] Automatic read length detection [20:33:07]...
As mentioned in https://github.com/HRGV/phyloFlash/issues/133, `phyloFlash_makedb.pl --remote` fails with the following error: ``` [17:36:19] Checking for required tools. [17:36:19] Using bowtiebuild found at "/opt/conda/envs/phyloflash/bin/bowtie-build". [17:36:19] Using grep found at "/usr/bin/grep". [17:36:19]...