flags.BoolVar(&cmd.skipOOO, "skip-ooo", false, "skip out-of-order tags")
priority := flags.Int("priority", 500, "container request priority")
pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
+ loglevel := flags.String("loglevel", "info", "logging threshold (trace, debug, info, warn, error, fatal, or panic)")
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
}()
}
+ lvl, err := log.ParseLevel(*loglevel)
+ if err != nil {
+ return 2
+ }
+ log.SetLevel(lvl)
+
if !cmd.runLocal {
runner := arvadosContainerRunner{
Name: "lightning import",
Client: arvados.NewClientFromEnv(),
ProjectUUID: cmd.projectUUID,
- RAM: 30000000000,
+ RAM: 60000000000,
VCPUs: 16,
Priority: *priority,
}
err = errors.New("cannot specify output file in container mode: not implemented")
return 1
}
- runner.Args = append([]string{"import", "-local=true", "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
+ runner.Args = append([]string{"import", "-local=true", "-loglevel=" + *loglevel, fmt.Sprintf("-skip-ooo=%v", cmd.skipOOO), "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
var output string
output, err = runner.Run()
if err != nil {
log.Printf("%s starting", infile)
defer log.Printf("%s done", infile)
tseqs, err := cmd.tileFasta(tilelib, infile)
- variants[0] = tseqs.Variants()
+ var kept, dropped int
+ variants[0], kept, dropped = tseqs.Variants()
+ log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
return err
}
infile2 := regexp.MustCompile(`\.1\.fasta(\.gz)?$`).ReplaceAllString(infile, `.2.fasta$1`)
log.Printf("%s starting", infile2)
defer log.Printf("%s done", infile2)
tseqs, err := cmd.tileFasta(tilelib, infile2)
- variants[1] = tseqs.Variants()
+ var kept, dropped int
+ variants[1], kept, dropped = tseqs.Variants()
+ log.Printf("%s found %d unique tags plus %d repeats", infile, kept, dropped)
return err
}
} else {
log.Printf("%s phase %d starting", infile, phase+1)
defer log.Printf("%s phase %d done", infile, phase+1)
tseqs, err := cmd.tileGVCF(tilelib, infile, phase)
- variants[phase] = tseqs.Variants()
+ var kept, dropped int
+ variants[phase], kept, dropped = tseqs.Variants()
+ log.Printf("%s phase %d found %d unique tags plus %d repeats", infile, phase+1, kept, dropped)
return err
}
}