Hi, I am having problems with Quast on the usegalaxy.eu server.
Have tried several times, but always get this warning:
WARNING: GeneMark tool can’t be started because of license limitations!
Also get this:
ERROR! Failed downloading bacteria database (url: https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently.
Any tip on how to solve this?
Hi @Roger_Meisal, can you file a bug report? You can do this by clicking on the ‘View or report this error’ button on the errored dataset (it looks like an insect).
Cheers, Simon
Hi Simon
Dataset does not produce any fatal error. Gene finding, Busco and Augustus does not seem to run. Here is the cut and paste from the log output of two try’s with slightly different settings
/usr/local/tools/_conda/envs/__quast@5.0.2/bin/quast -o outputdir --min-contig 500 --threads 1 --labels medaka_consensus_on_data_37_and_data_2__consensus --circos --gene-finding --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresh
/usr/local/tools/_conda/envs/__quast@5.0.2/bin/quast -o outputdir --min-contig 500 --threads 1 --labels medaka_consensus_on_data_37_and_data_2__consensus --circos --gene-finding --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /data/dnb02/galaxy_db/files/014/361/dataset_14361250.dat
Version: 5.0.2
System information:
OS: Linux-3.10.0-957.27.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core (linux_64)
Python version: 3.6.7
CPUs number: 10
Started: 2020-03-20 11:44:59
Logging to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/quast.log
CWD: /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working
Main parameters:
MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \
ambiguity: one, threshold for extensive misassembly size: 1000
Contigs:
Pre-processing...
/data/dnb02/galaxy_db/files/014/361/dataset_14361250.dat ==> medaka_consensus_on_data_37_and_data_2__consensus
2020-03-20 11:45:02
Running Basic statistics processor...
Contig files:
medaka_consensus_on_data_37_and_data_2__consensus
Calculating N50 and L50...
medaka_consensus_on_data_37_and_data_2__consensus, N50 = 5092083, L50 = 1, Total length = 5411235, GC % = 51.01, # N's per 100 kbp = 0.00
Drawing Nx plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/basic_stats/GC_content_plot.pdf
Drawing medaka_consensus_on_data_37_and_data_2__consensus GC content plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/basic_stats/medaka_consensus_on_data_37_and_data_2__consensus_GC_content_plot.pdf
Done.
2020-03-20 11:45:04
WARNING: GeneMark tool can't be started because of license limitations!
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
2020-03-20 11:45:04
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 2: Creating Icarus viewers...
2 of 2: Creating PDF with all tables and plots...
Done
2020-03-20 11:45:05
RESULTS:
Text versions of total report are saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/report.txt, report.tsv, and report.tex
Text versions of transposed total report are saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
HTML version (interactive tables and plots) is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/report.html
PDF version (tables and plots) is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/report.pdf
Icarus (contig browser) is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/icarus.html
Log is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410906/working/outputdir/quast.log
Finished: 2020-03-20 11:45:05
Elapsed time: 0:00:05.773240
NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0
Thank you for using QUAST!
/usr/local/tools/_conda/envs/__quast@5.0.2/bin/quast -o outputdir --min-contig 500 --threads 1 --labels medaka_consensus_on_data_37_and_data_2__consensus --k-mer-stats --k-mer-size 101 --circos --gene-finding --rna-finding --conserved-genes-finding --min
/usr/local/tools/_conda/envs/__quast@5.0.2/bin/quast -o outputdir --min-contig 500 --threads 1 --labels medaka_consensus_on_data_37_and_data_2__consensus --k-mer-stats --k-mer-size 101 --circos --gene-finding --rna-finding --conserved-genes-finding --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /data/dnb02/galaxy_db/files/014/361/dataset_14361250.dat
Version: 5.0.2
System information:
OS: Linux-3.10.0-957.27.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core (linux_64)
Python version: 3.6.7
CPUs number: 40
Started: 2020-03-20 11:21:05
Logging to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/quast.log
CWD: /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working
Main parameters:
MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \
ambiguity: one, threshold for extensive misassembly size: 1000
Contigs:
Pre-processing...
/data/dnb02/galaxy_db/files/014/361/dataset_14361250.dat ==> medaka_consensus_on_data_37_and_data_2__consensus
2020-03-20 11:21:22
Running Basic statistics processor...
Contig files:
medaka_consensus_on_data_37_and_data_2__consensus
Calculating N50 and L50...
medaka_consensus_on_data_37_and_data_2__consensus, N50 = 5092083, L50 = 1, Total length = 5411235, GC % = 51.01, # N's per 100 kbp = 0.00
Drawing Nx plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/basic_stats/GC_content_plot.pdf
Drawing medaka_consensus_on_data_37_and_data_2__consensus GC content plot...
saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/basic_stats/medaka_consensus_on_data_37_and_data_2__consensus_GC_content_plot.pdf
Done.
2020-03-20 11:21:32
WARNING: GeneMark tool can't be started because of license limitations!
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
2020-03-20 11:21:32
Running Barrnap...
Logging to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/predicted_genes/barrnap.log...
/usr/local/tools/_conda/envs/__quast@5.0.2/lib/python3.6/site-packages/quast_libs/barrnap/bin/barrnap \
--quiet -k bac --threads 1 outputdir/quast_corrected_input/medaka_consensus_on_data_37_and_data_2__consensus \
> outputdir/predicted_genes/medaka_consensus_on_data_37_and_data_2__consensus.rna.gff \
2>> outputdir/predicted_genes/barrnap.log
Ribosomal RNA genes = 22
Predicted genes (GFF): /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/predicted_genes/medaka_consensus_on_data_37_and_data_2__consensus.rna.gff
Done.
2020-03-20 11:22:13
Running BUSCO...
NOTICE: Permission denied accessing /usr/local/tools/_conda/envs/__quast@5.0.2/lib/python3.6/site-packages/quast_libs/augustus3.2.3. augustus will be downloaded to home directory /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/home/.quast
Downloading third-party tools...
Downloading augustus (file: augustus.tar.gz)...
augustus successfully downloaded!
Done
NOTICE: Permission denied accessing /usr/local/tools/_conda/envs/__quast@5.0.2/lib/python3.6/site-packages/quast_libs/busco. Busco databases will be downloaded to home directory /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/home/.quast
Downloading BUSCO database...
Downloading bacteria database (file: bacteria.tar.gz)...
ERROR! Failed downloading bacteria database (url: [https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz](https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz)), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/home/.quast/busco/bacteria.tar.gz and restart QUAST
WARNING: Failed to download bacteria database from [https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz](https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz) and unpack it into /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/home/.quast/busco
Failed finding conservative genes.
2020-03-20 11:24:46
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 2: Creating Icarus viewers...
2 of 2: Creating PDF with all tables and plots...
Done
2020-03-20 11:24:49
RESULTS:
Text versions of total report are saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/report.txt, report.tsv, and report.tex
Text versions of transposed total report are saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
HTML version (interactive tables and plots) is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/report.html
PDF version (tables and plots) is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/report.pdf
Icarus (contig browser) is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/icarus.html
Log is saved to /data/dnb02/galaxy_db/job_working_directory/007/410/7410776/working/outputdir/quast.log
Finished: 2020-03-20 11:24:50
Elapsed time: 0:03:45.030651
NOTICEs: 3; WARNINGs: 2; non-fatal ERRORs: 1
Thank you for using QUAST!
Hi Roger, unfortunately I don’t know enough about the tool to help you. I posted a link in the Gitter channel (https://gitter.im/usegalaxy-eu/Lobby) which tends to be a bit more active than this forum - hopefully someone will respond soon.