3_TSD_search output folder missing

[Wicker-Lab]

Hello,

First of all: thank you very much for the pipeline.

I ran the command like this:

nextflow run cgroza/GraffiTE --assemblies assemblies.csv --TE_library nrTREP20 --reference Bgt_genome_v3_16 --graph_method pangenie --genotype false

To detect SVs in 10 fully assembled genomes (so I didn't add any reads for mapping so far).

As far as I understood, the 3rd output folder TSD search and especially the pangenome.vcf should still be written, or not?

I only get: [rest_of_path]/out$ ls 1_SV_search 2_Repeat_Filtering

The output files in these folder look "normal" as far as I can tell. For example the file "indels.fa.masked" has many sequences, of which most are at least partially repeat masked.

However the file: genotypes_repmasked_filtered.vcf somehow has no variants, even if there are many in the per sample vcfs.

Also: there is not error message at the end of the run:

executor > local (21) [d3/6be117] process > map_asm (5) [100%] 9 of 9 ✔ [a0/d40a97] process > svim_asm (9) [100%] 9 of 9 ✔ [32/f5dfe6] process > survivor_merge [100%] 1 of 1 ✔ [9c/720983] process > repeatmask_VCF (1) [100%] 1 of 1 ✔ [4f/1f4338] process > tsd_prep (1) [100%] 1 of 1 ✔ [- ] process > tsd_search - [- ] process > tsd_report - Completed at: 25-Apr-2024 11:58:28 Duration : 26m 27s CPU hours : 2.3 Succeeded : 21

Thank you very much for your help!