blastn not running

[gbdias]

Hi,

The pipeline shows as completing successfully even though the BLASTN step is not running. Could you provide some tips to help troubleshoot this?

As this is failing silently I'm having a hard time understanding what is causing it.

[76/b0abd7] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP (asm)                    [100%] 1 of 1 ✔
[b5/388593] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK (asm)                    [100%] 1 of 1 ✔
[f2/bb15b0] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX (asm)                       [100%] 1 of 1 ✔
[c0/e6ad81] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK (asm)                  [100%] 1 of 1 ✔
[27/907f5b] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST (asm)                           [100%] 1 of 1 ✔
[94/7fd23b] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ (asm.fa)                      [100%] 1 of 1 ✔
[51/4e303d] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK (asm)                    [100%] 1 of 1 ✔
[aa/04b591] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON (asm)                         [100%] 1 of 1 ✔
[-        ] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                               -
[8a/dbabdc] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK (asm)                  [100%] 1 of 1 ✔
[d1/060fdc] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS (asm)           [100%] 1 of 1 ✔
[62/3ca57d] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT (asm)                 [100%] 1 of 1 ✔
[52/7099b9] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS (asm)           [100%] 1 of 1 ✔
[bc/a0fd6d] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR (asm)             [100%] 1 of 1 ✔
[d5/449b3c] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR (asm)             [100%] 1 of 1 ✔
[ea/ab86f1] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY (asm)                        [100%] 1 of 1 ✔
[34/1ce488] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES (asm_blob)                         [100%] 3 of 3 ✔
[2f/a5512d] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA (asm)         [100%] 1 of 1 ✔
[73/a3adc4] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR (asm)                [100%] 1 of 1 ✔
[0f/a5fa9d] SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                               [100%] 1 of 1 ✔
-[sanger-tol/blobtoolkit] Pipeline completed successfully-
Completed at: 20-Aug-2025 07:09:18
Duration    : 13h 40m 51s
CPU hours   : 499.6
Succeeded   : 55

Here is my run command:

nextflow run sanger-tol/blobtoolkit \
       --input samplesheet.csv \
       --fasta asm.fa \
       --outdir "$RESULTS" \
       -params-file workflow_parameters.yml \
       --project uppmax2025-2-58 \
       -profile uppmax \
       -resume

here is the workflow_parameters.yml

project: 'uppmax2025-2-58'
input: 'samplesheet.csv'
align: true
taxon: 470658
fasta: 'asm.fa'
blastp: '/proj/snic2022-6-208/private/martin/databases/uniprot_2025_07/reference_proteomes.dmnd'
blastx: '/proj/snic2022-6-208/private/martin/databases/uniprot_2025_07/reference_proteomes.dmnd'
blastn: '/proj/snic2022-6-208/private/martin/databases/nt_2025_07'
taxdump: '/proj/snic2022-6-208/private/martin/databases/taxdump_2025_07'
busco: '/sw/data/BUSCO_data/latest/rackham/v5_lineage_sets'
busco_lineages: 'insecta_odb10'

[muffato]

Hi @gbdias . This isn't necessarily an issue. BLAST_BLASTN is only meant to run if BLASTN_TAXON couldn't find any hit.

What do you mean by "As this is failing silently" ?

[gbdias]

Hi @muffato,

In my results I only have taxonomy assignments based on buscogenes, so many shorter contigs show as "no-hit" because they do not contain BUSCO genes. Based on this (and on that fact that the BLAST_BLASTN process didn't run) I assumed that the pipeline didn't run correctly because I expected to see bestsum_order, bestsum_class etc, and not just buscogenes_order, buscogenes_class.

[gbdias]

in the .nextflow.log file I do see this line:

Aug-19 17:28:31.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN

Although the process never seems to have finished, or failed.

And for the BLASTN_TAXON, it does finish, although I do not see any blast results in the blobdir

~> TaskHandler[jobId: 38621; id: 35; name: SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON (asm); status: RUNNING; exit: -; error: -; workDir: /crex/proj/snic2021-6-194/BGE-Platycleis_falx-2025-assembly/analyses/05_btk/work/aa/04b59146b0c1f9454124f5f898e3a5 started: 1755623105663; exited: -; ]
Aug-20 06:59:17.897 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 38621; id: 35; name: SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON (asm); status: COMPLETED; exit: 0; error: -; workDir: /crex/proj/snic2021-6-194/BGE-Platycleis_falx-2025-assembly/analyses/05_btk/work/aa/04b59146b0c1f9454124f5f898e3a5 started: 1755623105663; exited: 2025-08-20T04:59:13Z; ]

[muffato]

in the .nextflow.log file I do see this line:

Aug-19 17:28:31.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN

Although the process never seems to have finished, or failed.

And for the BLASTN_TAXON, it does finish, although I do not see any blast results in the blobdir

~> TaskHandler[jobId: 38621; id: 35; name: SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON (asm); status: RUNNING; exit: -; error: -; workDir: /crex/proj/snic2021-6-194/BGE-Platycleis_falx-2025-assembly/analyses/05_btk/work/aa/04b59146b0c1f9454124f5f898e3a5 started: 1755623105663; exited: -; ]
Aug-20 06:59:17.897 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 38621; id: 35; name: SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON (asm); status: COMPLETED; exit: 0; error: -; workDir: /crex/proj/snic2021-6-194/BGE-Platycleis_falx-2025-assembly/analyses/05_btk/work/aa/04b59146b0c1f9454124f5f898e3a5 started: 1755623105663; exited: 2025-08-20T04:59:13Z; ]

This .nextflow.log is fine. DEBUG nextflow.processor.TaskProcessor - Starting process only means that Nextflow has identified that the pipeline contains a process named SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN after parsing the code. In the log you should see this line is part of a block where all the steps of the pipeline are listed, whether or not they will see data actually coming through.

Job submission is indicated in the log file by Submitted process (or in all lower case submitted process). Job completion is indicated by Task completed (with the exit code on the same line).

@rjchallis : can you please comment on the other comment #195 (comment) ?

[northernpikee]

Hello! I experienced the same problem. To get more hits, I changed the taxrule in the updateBlobDir script from buscoregions to bestsumorder so that shorter contigs could get taxonomic annotations.