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after just skipping the kmerfinder my pipline runs...
# bacass
a
after just skipping the kmerfinder my pipline runs successfully: executor > local (2) [13/7284fa] NFCORE_BACASSBACASSNANOPLOT (longreads) [100%] 1 of 1, cached: 1 ✔️ [- ] NFCORE_BACASSBACASSPYCOQC - [9c/c6ce1f] NFCORE_BACASSBACASSPORECHOP_PORECHOP (longreads) [100%] 1 of 1, cached: 1 ✔️ [- ] NFCORE_BACASSBACASSCANU - [- ] NFCORE_BACASSBACASSMEDAKA - [e3/1b5237] NFCORE_BACASSBACASSKRAKEN2_DB_PREPARATION (k2_viral_20240112) [100%] 1 of 1, cached: 1 ✔️ [- ] NFCORE_BACASSBACASSKRAKEN2 - [88/53a7db] NFCORE_BACASSBACASSKRAKEN2_LONG (longreads) [100%] 1 of 1 ✔️ [- ] NFCORE_BACASSBACASSQUAST - [- ] NFCORE_BACASSBACASSGUNZIP - [- ] NFCORE_BACASSBACASSPROKKA - [67/480750] NFCORE_BACASSBACASSMULTIQC_CUSTOM (1) [100%] 1 of 1 ✔️ -[nf-core/bacass] Pipeline completed successfully- but the assembly step is skipped?? Again, any help is very much appreciated!!
j
moreinfo
s
To help we'd love a few more details please: 1. The Nextflow command you used to launch the pipeline 2. Any custom Nextflow config files 3. The full error message 4. The corresponding 
.nextflow.log
file, where you are running the analysis. Remember to use triple backslashes on their own lines for code blocks. Also take a look at https://nf-co.re/usage/troubleshooting for more information on debugging failed pipelines. Thanks!
a
what more info do you need? here is my command: nextflow run nf-core/bacass --input samplesheet.tsv -profile docker --assembly_type long --kraken2db “https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20240112.tar.gz” --outdir P60_nf --skip_kmerfinder --assembler canu --canu_mode=“-nanopore” --ncbi_assembly_metadata assembly_summary_genbank.txt --max_memory 60GB -resume
j
Oh, did you not see the Slackbot response?
image.png
moreinfo
is meant to be a keyword
party dino 1
s
To help we'd love a few more details please: 1. The Nextflow command you used to launch the pipeline 2. Any custom Nextflow config files 3. The full error message 4. The corresponding 
.nextflow.log
file, where you are running the analysis. Remember to use triple backslashes on their own lines for code blocks. Also take a look at https://nf-co.re/usage/troubleshooting for more information on debugging failed pipelines. Thanks!
j
to post an automated message, do you not see it?
I think ti might be a bug... given you're skipping kmerfinder could you try your command again but with 
--kmerfinderdb false
? OTherwise you might have to wait until @Daniel_VM is backf rom holiday, unless @Daniel Straub knows?
a
i reran it using kmerfinderdb which i got to work, however canu is still skipped?
no it looks like this: executor > local (8) [fd/e23907] NFCORE_BACASSBACASSNANOPLOT (longreads) [100%] 1 of 1 ✔️ [- ] NFCORE_BACASSBACASSPYCOQC - [b9/329040] NFCORE_BACASSBACASSPORECHOP_PORECHOP (longreads) [100%] 1 of 1 ✔️ [- ] NFCORE_BACASSBACASSCANU - [- ] NFCORE_BACASSBACASSMEDAKA - [50/79f1f1] NFCORE_BACASSBACASSKRAKEN2_DB_PREPARATION (k2_viral_20240112) [100%] 1 of 1 ✔️ [- ] NFCORE_BACASSBACASSKRAKEN2 - [0d/ef2322] NFCORE_BACASSBACASSKRAKEN2_LONG (longreads) [100%] 1 of 1 ✔️ [cb/d9ea6a] NFCORE_BACASSBACASSKMERFINDER_SUBWORKFLOW:UNTAR (20190108_kmerfinder_stable_dirs.tar.gz) [100%] 1 of 1 ✔️ [b9/0822c1] NFCORE_BACASSBACASSKMERFINDER_SUBWORKFLOW:KMERFINDER (longreads) [100%] 1 of 1 ✔️ [32/49a843] NFCORE_BACASSBACASSKMERFINDER_SUBWORKFLOW:KMERFINDER_SUMMARY (kmerfinder_summary) [100%] 1 of 1 ✔️ [- ] NFCORE_BACASSBACASSKMERFINDER_SUBWORKFLOW:FIND_DOWNLOAD_REFERENCE - [- ] NFCORE_BACASSBACASSQUAST - [- ] NFCORE_BACASSBACASSQUAST_BYREFSEQID - [- ] NFCORE_BACASSBACASSGUNZIP - [- ] NFCORE_BACASSBACASSPROKKA - [81/56be6d] NFCORE_BACASSBACASSMULTIQC_CUSTOM (1) [100%] 1 of 1 ✔️ -[nf-core/bacass] Pipeline completed successfully- Completed at: 01-Oct-2024 100010 Duration : 6m 9s CPU hours : 0.8 Succeeded : 8 any idea why it skips canu??
even in the options print before it prints this: Assembly parameters assembler : canu assembly_type : long canu_mode : -nanopore so i dont understand why it doenst do anything?
j
I'm not sure sorry, I'm not familiar that with the pipeline 😞 we will have to wait from the developers
d
Hello @Anke King sorry for the late reply. Could you check if this error is addressed in #164 (there are two PRs related to this issue, one for Canu)? If so, it should be fixed in 
dev
. To test it add 
-r dev
to your nextflow run command.
a
that worked, thanks!
party dino 1
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