Closed VibrantStarling closed 4 years ago
meren
commented
4 years ago Hi,
Can you open an R terminal and then type library(tidyverse)? Probably there is an error and it can't be properly loaded.
This happened to me, and then I was able to solve it by installing r-stringi through conda.
Please try and let me know.
Best,
VibrantStarling
commented
4 years ago Thanks meren,
I downlaoded r-stringi and now the tidyverse and qvalue errors are gone, but now I'm back to pyANI giving me a non zero sum and the mini test still gives me the same error as before...
library(tidyverse) gives me this:
Running tidy verse
> library(tidyverse)
Registered S3 method overwritten by 'rvest':
method from
read_xml.response xml2
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.2.1 ✔ purrr 0.3.2
✔ tibble 2.1.3 ✔ dplyr 0.8.0.1
✔ tidyr 0.8.3 ✔ stringr 1.4.0
✔ readr 1.3.1 ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()pangenomic suite errors
Config Error: PyANI returned with non-zero exit code, there may be some errors. please check
the log file for details.
Config Error: According to the exit code ('255'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less. mini suite errors
Config Error: According to the exit code ('-2'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less. Couple of extra bits, I don't know if they will help. Here is what the pangenomic test and the out put during the pyANI run and what's in the ANI_LOG.txt file for it
Anvi'o will use 'PyANI' by Pritchard et al. (DOI: 10.1039/C5AY02550H) to compute
ANI. If you publish your findings, please do not forget to properly credit their
work.
[PyANI] Num threads to use ...................: 1
[PyANI] Alignment method .....................: ANIb
[PyANI] Log file path ........................: /tmp/tmpy5mx_ket/test-output/pan_test/ANI_LOG.txt
[12 Nov 19 18:59:29 PyANI] Running ...
✖ anvi-compute-genome-similarity encountered an error after 0:00:04.195145GNU nano 2.2.6 File: ANI_LOG.txt
DATE: 12 Nov 19 18:59:29
CMD LINE: average_nucleotide_identity.py --outdir output $
Traceback (most recent call last):
File "/pub28/helend/miniconda3/envs/anvio-6/bin/average_n$
results = methods[args.method][0](infiles, org_lengths)
File "/pub28/helend/miniconda3/envs/anvio-6/bin/average_n$
fraglengths=fraglengths, mode=args.method)
File "/pub28/helend/miniconda3/envs/anvio-6/lib/python3.6$
resultvals = parse_blast_tab(blastfile, fraglengths, mo$
File "/pub28/helend/miniconda3/envs/anvio-6/lib/python3.6$
data = pd.DataFrame.from_csv(filename, header=None, sep$
AttributeError: type object 'DataFrame' has no attribute 'f$
You have the wrong version of pyANI.
Please make sure it is 0.2.9 and pandas is 0.23.1. you can enforce them to be like that by running
pip install pandas==0.23.1
pip install pyani==0.2.9Ah, thanks for spotting that!
Updated it and I'm still getting the -2 error for both tests now, but the 255 errors have gone away. Thanks!
Do you know what the -2 error refers to and do I need to worry about it?
meren
commented
4 years ago @VibrantStarling,
Do you know what the -2 error refers to and do I need to worry about it?
I am not sure really :) Do things seem to work when you actually create a pangenome?
vinisalazar
commented
4 years ago I would just like to report that I went through the same problems and installing the correct versions for pandas, pyani, cherrypy, django and h5py (referred in #1258 ) solved it. Would be great to have the fix in the next conda release!
VibrantStarling
commented
4 years ago yes things seem to work now! Thanks meren
THIS IS A TECHNICAL ISSUE
Hello,
I'm having trouble installing anvio-6.1 on a debian 7 remote server.
I followed the instructions here: https://github.com/merenlab/anvio/issues/1258 because I was having an issue with quite a few of the packages not being included, or in the wrong version from your conda download. I had to run separate downloads for pandas, pyani, cherrypy, django, tidyverse, bioconductor-qvalue, hy5py and r-optparse.
When I run the mini self test it spits out the config error -2, but completes the test (I think) and runs through to the interactive in terminal pages.
When I run the pangenomics self test it spits out config error 255 and this:
HOWEVER both r-tidyverse and bioconductor-qvalue are installed (see the list of packages below)
I've attached the output for both the tests and highlighted stuff that could be important in a pdf at the bottom of this (otherwise this message would be WAY too long)
Send help
Thanks
packages list
anvio-self-self-test-errors.pdf