No .insert.fasta output when providing --primers and --insert_reference

drabitoris commented 7 months ago

Ask away!

Hi team,

Thanks for updating this pipeline! I've just run v1.2.0 with parameters --primers and --insert_reference, while there is no .insert.fasta found under the output directory or relevant info in the report (the output directory and the report look the same as those without using --primers and --insert_reference). It shows in the log that it did perform 'findPrimers' and 'inserts' though:

executor >  slurm (871)
[53/5c8f37] process > validate_sample_sheet          [100%] 1 of 1 ✔
[45/79e3bf] process > fastcat (96)                   [100%] 96 of 96 ✔
[a3/7b3b6e] process > pipeline:checkIfEnoughReads... [100%] 96 of 96 ✔
[0d/7f3766] process > pipeline:assembleCore (21)     [100%] 88 of 88, failed:...
[e2/ae9135] process > pipeline:lookup_medaka_mode... [100%] 1 of 1 ✔
[66/01fe1e] process > pipeline:medakaPolishAssemb... [100%] 82 of 82 ✔
[52/056e0c] process > pipeline:downsampledStats (83) [100%] 83 of 83 ✔
[d1/705acf] process > pipeline:findPrimers (11)      [100%] 82 of 82 ✔
[8c/c0c1eb] process > pipeline:medakaVersion         [100%] 1 of 1 ✔
[d9/f19aa8] process > pipeline:flyeVersion           [100%] 1 of 1 ✔
[39/a4ec3a] process > pipeline:getVersions           [100%] 1 of 1 ✔
[9c/cc4666] process > pipeline:getParams             [100%] 1 of 1 ✔
[e7/957be2] process > pipeline:inserts               [100%] 1 of 1 ✔
[98/6e6629] process > pipeline:assembly_qc (11)      [100%] 82 of 82 ✔
[-        ] process > pipeline:insert_qc             -
[be/8a8c66] process > pipeline:runPlannotate (1)     [100%] 1 of 1 ✔
[02/40a5d4] process > pipeline:assemblyMafs (10)     [100%] 82 of 82 ✔
[72/823c00] process > pipeline:report (1)            [100%] 1 of 1 ✔
[75/c94fce] process > output (88)                    [100%] 171 of 171 ✔
Completed at: 26-Apr-2024 13:17:53
Duration    : 26m 11s
CPU hours   : 13.0 (0.9% failed)
Succeeded   : 866
Failed      : 5

May you please help me with this? Many thanks!

sarahjeeeze commented 6 months ago

Hi, thanks for reporting this. Have you had success with the same data set with previous version of the workflow?

Can you find or see the primers specified in the final assemblies?

sarahjeeeze commented 5 months ago

closing through lack of response

epi2me-labs / wf-clone-validation

No .insert.fasta output when providing --primers and --insert_reference #45

Ask away!