Comments (4)
Hi Peter,
Thanks for noticing this bug! We already fixed it and the fix will be included in MetaQuast 3.1which we plan to release by the end of this week.
You can check out release_3.1 branch now.
The bug occured only in case number of references is less than number of assemblies (which is not common for metagenomes actually).
from quast.
Thank you Alexey for the fast answer but I just checked out the 3.1 version and I think this time it is another bug:
Summarizing results...
[Errno 2] No such file or directory: '/home/pbelmann/metrics/workspace/5489634d60b2b261463f0207/bioboxes/quast/cache/not_aligned_quast_output/transposed_report.tsv'
Traceback (most recent call last):
File "/usr/local/quast/metaquast.py", line 706, in <module>
return_code = main(sys.argv[1:])
File "/usr/local/quast/metaquast.py", line 694, in main
create_meta_summary.do(output_dirpath, summary_dirpath, metrics_for_plots, misassembl_metrics, ref_names)
File "/usr/local/quast/libs/create_meta_summary.py", line 75, in do
results, all_rows, cur_ref_names = get_results_for_metric(ref_names, metric, contigs_num, labels, output_dirpath, qconfig.transposed_report_prefix + '.tsv')
File "/usr/local/quast/libs/create_meta_summary.py", line 30, in get_results_for_metric
results_file = open(results_fpath, 'r')
IOError: [Errno 2] No such file or directory: '/home/pbelmann/metrics/workspace/5489634d60b2b261463f0207/bioboxes/quast/cache/not_aligned_quast_output/transposed_report.tsv'
I'm using about 20 references and two assembly files.
from quast.
Peter, thanks again! Sorry for the inconvenience it was our fault, the bug is fixed just now. This didn't depend on number of refs and assemblies (I hope nothing more is dependent on it), this was caused by another rare case: everything aligned, so there were no report for "not_aligned_quast_output" at all. Now we process this situation correctly!
from quast.
thx it works now 👍
from quast.
Related Issues (20)
- ERROR! File not found (contigs) running on biocontainers/quast:5.2.0 HOT 4
- MetaQUAST 5.2.0 reference genome "not in list" error when "Summarizing results..."
- metaquast coloring error for > 14 samples
- OSError: [Errno 22]
- Error creating Krona plots in metaquast.py HOT 8
- Version of installed minimap2 differs from its version in the QUAST package (2.24) HOT 1
- Augustus busco not running with a conda install
- ERROR! Skipping S7KLEB_S14_L001_R2_001.fastq.00.0_0.cor.fastq.gz because it contains non-ACGTN characters. HOT 1
- [Errno 30] Read-only file system: '/usr/local/lib/python3.10/dist-packages/quast_libs/bwa/make.log' HOT 2
- Issues with the installation
- Issues about 'quast-download-busco' HOT 2
- minimap2 cannot works correctly in the "Running Contig Analyzer" step
- Error occured while running Busco HOT 2
- No space left on device HOT 5
- Bam files in output HOT 1
- What size of genome fraction can be considered low?
- Issues running quast.
- invalid literal for int() with base 10: 'START_A'
- mapped reads count in reads_report
- License issue
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 quast.