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vg mpmap writes log messages to stdout
1. What were you trying to do?
make a .gamp file by redirecting vg mpmap output to a file
2. What did you want to happen? A correctly formatted GAMP file to be created, even when progress log is not suppressed
3. What actually happened?
A corrupted GAMP file got created due to log output being written to stdout instead of stderr. including -p parameter fixes the issue as it suppresses log output completely.
4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
5. What data and command can the vg dev team use to make the problem happen?
vg mpmap -x x.xg -g x.gcsa --fastq x.fq --output-fmt GAMP --read-length very-short -n dna > mapped.gamp
6. What does running vg version say?
1.66.0