Bug report: option parsing error

[JianjunJin]

Test Data

• the assembly graph file: snp.graph.gfa.txt
• a single-read file: test_reads.11_13946.fastq.txt

Error

GraphAligner -g snp.graph.gfa -f test_reads.11_13946.fastq -x vg -a test.gaf --seeds-mum-count -1

GraphAligner bioconda 1.0.17- GraphAligner bioconda 1.0.17- pick only one seeding method run with option -h for help

Description

When I used the option --seeds-mum-count -1, GraphAligner died with the following error pick only one seeding method.

Temporary Solution

By looking at the code, I find a temporary solution to be turning off all other seeding methods, such as

GraphAligner -g snp.graph.gfa -f test_reads.11_13946.fastq -x vg -a test.gaf --seeds-mum-count -1 --seeds-mem-count 0 --seeds-minimizer-densit 0

GraphAligner bioconda 1.0.17- GraphAligner bioconda 1.0.17- Load graph from snp.graph.gfa Build MUM/MEM seeder from the graph Build alignment graph MUM seeds, min length 20 Seed cluster size 1 Extend up to 5 seed clusters Alignment bandwidth 5, tangle effort 10000 Clip alignment ends with identity < 66% X-drop DP score cutoff 14705 Backtrace from 10 highest scoring local maxima per cluster write alignments to test.smd.mtc.gaf Align Alignment finished Input reads: 1 (15009bp) Seeds found: 183 Seeds extended: 2 Reads with a seed: 1 (15009bp) Reads with an alignment: 1 (14824bp) Alignments: 1 (14824bp) End-to-end alignments: 0 (0bp)

Please let me know any other information you need.

[maickrau]

The preset -x vg already picks minimizer seeding, and then picking MUM seeding gives the error. You can indeed disable minimizer seeding by explicitly adding --seeds-minimizer-density 0. My recommendation is to either use a preset or completely custom parameters, but not mix them.

[Kinggerm]

I see. Thank you!