Comments (7)
I am working on this bioconda/bioconda-recipes#38875
from pggb.
After a manual copy I get
(pggb) [heumos@savasana ~]$ partition-before-pggb -i ~/git/pggb/data/HLA/DRB1-3123.fa.gz -o test_partition -n 12 -t 16 -p 70
[wfmash::map] Reference = [/home/heumos/git/pggb/data/HLA/DRB1-3123.fa.gz]
[wfmash::map] Query = [/home/heumos/git/pggb/data/HLA/DRB1-3123.fa.gz]
[wfmash::map] Kmer size = 19
[wfmash::map] Window size = 30
[wfmash::map] Segment length = 5000 (read split allowed)
[wfmash::map] Block length min = 25000
[wfmash::map] Chaining gap max = 100000
[wfmash::map] Percentage identity threshold = 70%
[wfmash::map] Skip self mappings
[wfmash::map] Mapping output file = /dev/stdout
[wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[wfmash::map] Execution threads = 16
[wfmash::skch::Sketch::build] minimizers picked from reference = 10970
[wfmash::skch::Sketch::index] unique minimizers = 2797
[wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 19) ... (22, 1)
[wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, consider all minimizers during lookup.
[wfmash::map] time spent computing the reference index: 0.015768 sec
[wfmash::skch::Map::mapQuery] mapped 100.00% @ 3.25e+05 bp/s elapsed: 00:00:00:00 remain: 00:00:00:00
[wfmash::skch::Map::mapQuery] count of mapped reads = 11, reads qualified for mapping = 12, total input reads = 12, total input bp = 163416
[wfmash::map] time spent mapping the query: 5.04e-01 sec
[wfmash::map] mapping results saved in: /dev/stdout
wfmash -s 5000 -l 25000 -p 70 -n 11 -k 19 -H 0.001 -X -t 16 --tmp-base test_partition /home/heumos/git/pggb/data/HLA/DRB1-3123.fa.gz --approx-map
0.39s user 2.04s system 461% cpu 0.52s total 69280Kb max memory
python3 /home/heumos/miniconda3/envs/pggb/bin/scripts/paf2net.py -p test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf
0.02s user 0.00s system 95% cpu 0.02s total 10044Kb max memory
Traceback (most recent call last):
File "/home/heumos/miniconda3/envs/pggb/bin/scripts/net2communities.py", line 19, in <module>
import igraph as ig
ModuleNotFoundError: No module named 'igraph'
Command exited with non-zero status 1
python3 /home/heumos/miniconda3/envs/pggb/bin/scripts/net2communities.py -e test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf.edges.list.txt -w test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf.edges.weights.txt -n test_partition/DRB1-3123.fa.gz.6deb21e.mappings.wfmash.paf.vertices.id2name.txt --accurate-detection --output-prefix test_partition/DRB1-3123.fa.gz.6deb21e
0.01s user 0.00s system 95% cpu 0.02s total 10164Kb max memory
from pggb.
Dependencies, dependencies everywhere.
What did you do exactly with the 'manual copy'?
from pggb.
mkdir /home/heumos/miniconda3/envs/pggb/bin/scripts
cp ~/git/pggb/scripts/* /home/heumos/miniconda3/envs/pggb/bin/scripts/
from pggb.
I did a new installation bioconda/bioconda-recipes#38875, but the scripts directory is still missing essential scripts:
ls /home/heumos/miniconda3/envs/pggb/bin/scripts
nucmer2vcf.R vcf_preprocess.sh
To confirm I installed the correct conda package I did:
igraph
No configuration file, using defaults
igraph 0.10.3 running inside Python 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:23:14) [GCC 10.4.0] on linux
from pggb.
What you currently have:
mv pggb $PREFIX/bin
mv partition-before-pggb $PREFIX/bin
mv scripts/*.py $PREFIX/bin
mv scripts $PREFIX/bin
Since you already moved the Python scripts, they won't be in the scripts folder anymore. So I would suggest:
mv pggb $PREFIX/bin
mv partition-before-pggb $PREFIX/bin
cp scripts/*.py $PREFIX/bin
mv scripts $PREFIX/bin
Also please add a tiny test so we can detect such errors while packaging.
from pggb.
Finally, it works :)
from pggb.
Related Issues (20)
- empty VCF after running PanGenIe on the pggb assembly HOT 1
- GFA with no P lines HOT 5
- DRB1-3123 example not producing a nice graph anymore after `biwflambda` update. HOT 5
- PGGB use case with hexaploidy genomes HOT 1
- force reference output in VCF HOT 2
- Three chromosome take too long time HOT 16
- High heterogeneity in sequences identity HOT 2
- extracting node path-coverage information HOT 3
- wfmash -Y option HOT 3
- About the result study HOT 4
- Question about the example "scerevisiae7.fasta.gz " HOT 1
- ValueError: too many values to unpack (expected 13) HOT 3
- Annotating the 1D pangenome graph visualisation with centromere coordinates
- Get the fasta file of non reference sequence
- [W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.) HOT 4
- PGGB get the fasta file of non reference sequence
- Building a graph from fragmented assemblies
- interoperability with vg - error:[vg::SmallSnarlSimplifier] Invalid graph on iteration 0 HOT 14
- Possible community detection bug HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pggb.