NextDenovo will not load and run a dataset due to the tool being outdated. It keeps pushing a message to update the tool to the next version. It is currently v2.5.0, it states that it needs to be v2.5.2.
Welcome @ellazdc
Would you be able to share more about how you are using the tool and where?
A few questions
- What is the full name and version of the tool? Find this at the top of the tool form.
- Are you working at UseGalaxy.eu or a different server?
- What is reported on your Job Information Details page for one of the red error datasets? Full input/parameter table and all logs (click to expand each).
- Or, does the tool not submit at all?
If you would like to generate a share link to your history and post it back here in your reply, all of these details will be included! You can unshare after we are done.
With that context, for this type of message in the Tool Standard Output logs with this tool, it is just a warning and can be ignored! All of the job dependencies are handled by Galaxy. Even very old tools can usually run Ok!
Instead, you’ll probably find a more descriptive problem about what is going on in the other log message, the Tool Standard Error. You might need to click to expand to read the full message. This is coming from the underlying tool! Assembly is a complex process, and while we don’t have a Galaxy tutorial that uses this tool, we do have many single cell tutorials, including QA/QC paths that will likely be important. If interested, see → 
Single Cell / Tutorial List
Let’s start there, and let us know if you solve this or if you would like some help! 
- NextDenovo: string graph-based de novo assembler for long reads; Galaxy Version 2.5.0+galaxy0
- Galaxy EU
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[29 INFO] 2026-04-10 00:35:12 NextDenovo start... [29 INFO] 2026-04-10 00:35:12 version:v2.5.0 logfile:pid29.log.info [29 WARNING] 2026-04-10 00:35:12 Re-write workdir [29 INFO] 2026-04-10 00:35:12 skip mkdir: /data/jwd08/main/099/804/99804503/working [29 INFO] 2026-04-10 00:35:12 mkdir: /data/jwd08/main/099/804/99804503/working/01.raw_align [29 INFO] 2026-04-10 00:35:12 mkdir: /data/jwd08/main/099/804/99804503/working/02.cns_align [29 INFO] 2026-04-10 00:35:12 mkdir: /data/jwd08/main/099/804/99804503/working/03.ctg_graph [29 INFO] 2026-04-10 00:35:17 Total jobs: 1 [29 INFO] 2026-04-10 00:35:17 Submitted jobID:[30] jobCmd:[/data/jwd08/main/099/804/99804503/working/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle. [29 INFO] 2026-04-10 00:37:29 db_stat done [29 INFO] 2026-04-10 00:37:29 updated options: rerun: 3 task: all deltmp: 1 rewrite: 1 read_type: clr job_type: local input_type: raw genome_size: 1g seed_depth: 5.59 parallel_jobs: 24 read_cutoff: 1000 pa_correction: 24 seed_cutfiles: 24 seed_cutoff: 1001 blocksize: 10000000 job_prefix: nextDenovo ctg_cns_options: -p 24 minimap2_options_map: -x map-pb sort_options: -m 128g -t 24 -k 40 -l 300 -k 0 workdir: /data/jwd08/main/099/804/99804503/working correction_options: -p 24 -max_lq_length 1000 -min_len_seed 500 input_fofn: /data/jwd08/main/099/804/99804503/working/input.fofn raw_aligndir: /data/jwd08/main/099/804/99804503/working/01.raw_align cns_aligndir: /data/jwd08/main/099/804/99804503/working/02.cns_align ctg_graphdir: /data/jwd08/main/099/804/99804503/working/03.ctg_graph minimap2_options_cns: -t 24 -x ava-pb -k 17 -w 17 --minlen 100 --maxhan1 500 minimap2_options_raw: -t 24 --minlen 500 --minmatch 100 --minide 0.05 --kn 17 --wn 10 --cn 20 --maxhan1 5000 --maxhan2 500 -x ava-pb nextgraph_options: -a 1 -E 1000 -q 0 -i 0.1 -I 0.7 -R 0.0 -S 0.4 -r 0.5 -M 0.9 -T 0.6 -N 2 -u 2 -w 3 -D 2 -P 2 -m 1.5 -n 2000.0 -B 500 -C 20 -z 8 -l 15 -L 5 -t 500 -F 1000 [29 INFO] 2026-04-10 00:37:29 summary of input data: file:e[35m /data/jwd08/main/099/804/99804503/working/01.raw_align/input.reads.stat e[0m [Read length stat] Types Count (#) Length (bp) N10 22906 18830 N20 57667 14084 N30 102438 11181 N40 158297 9007 N50 227647 7235 N60 314786 5697 N70 427384 4329 N80 579832 3100 N90 803761 1997 Types Count (#) Bases (bp) Depth (X) Raw 1976809 5997438091 6.00 Filtered 783194 403869487 0.40 Clean 1193615 5593568604 5.59 *Suggested seed_cutoff (genome size: 1000.00Mb, expected seed depth: 45, real seed depth: 5.59): 1001 bp e[35m*NOTE:e[0m The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully. Of course, it's better to sequencing more longer reads and try again. [29 ERROR] 2026-04-10 00:37:29 e[35mthe input data is insufficient for an assembly.e[0m
Thanks for sharing! The important part is at the bottom in the last few lines, but do go back reference the other metrics at the top of the log as you work through this each time while tuning.
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Suggested seed_cutoff (genome size: 1000.00Mb, expected seed depth: 45, real seed depth: 5.59): 1001 bp
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NOTE: The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully. Of course, it’s better to sequencing more longer reads and try again.
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ERROR: the input data is insufficient for an assembly.
It looks like you will need to explore the parameters a bit more to get a successful assembly! The assembler is reporting that your data looks too sparse for the current seed settings. You can try using defaults to start with and build up from there.
The tool authors host tutorials and a parameter reference at their Github here → GitHub - Nextomics/NextDenovo: Fast and accurate de novo assembler for long reads · GitHub
Hope this helps!
1 Like
I understand, thank you for your help