Empty alignment gaf output

[abanerjee10]

I get empty output gaf files when aligning reads to genome graphs. How do I resolve this issue?

Data: vg_toy_x.zip Command: minigraph -t 24 -cx lr vg_toy_x.gfa vg_toy_x.fastq

[colindaven]

You've set parameters for long reads
-cx lr

but the toy example has one short read, so you need 
-cx sr

[abanerjee10]

Sorry, I tried both arguments and pasted the command with long read mode. Both give me empty output gafs.

Data: vg_toy_x.zip

Commands: minigraph -t 24 -cx sr vg_toy_x.gfa vg_toy_x.fastq minigraph -t 24 -cx lr vg_toy_x.gfa vg_toy_x.fastq

Output: [M::main::0.001*3.34] loaded the graph from "vg_toy_x.gfa" [M::mg_index::0.003*4.91] indexed the graph [M::mg_opt_update::0.004*4.82] occ_max1=50; lc_max_occ=2 [M::worker_pipeline::0.005*3.85] mapped 2 sequences [M::main] Version: 0.20-r559 [M::main] CMD: minigraph -t 24 -cx lr vg_toy_x.gfa vg_toy_x.fastq [M::main] Real time: 0.005 sec; CPU: 0.019 sec; Peak RSS: 0.002 GB

I have the same error for larger genome graphs with short and long reads that I can't upload due to file sizes.

[Szhiha]

I have the same issue.

[aleixcanalda]

@Szhiha I had the same problem but apparently the problem is with the v20 release (@lh3 not sure if this was intentional or not?). If you use minigraph-v19, -xsr does work