Compiling galah v0.3.1 (https://github.com/wwood/galah#68e920b8)
error[E0308]: mismatched types
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:332:19
    |
332 |     set_log_level(m, true, program_basename, program_version);
    |     ------------- ^ expected struct `clap::parser::matches::arg_matches::ArgMatches`, found struct `ArgMatches`
    |     |
    |     arguments to this function are incorrect
    |
    = note: struct `ArgMatches` and struct `clap::parser::matches::arg_matches::ArgMatches` have similar names, but are actually distinct types
note: struct `ArgMatches` is defined in crate `clap`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-3.2.23/src/parser/matches/arg_matches.rs:68:1
    |
68  | pub struct ArgMatches {
    | ^^^^^^^^^^^^^^^^^^^^^
note: struct `clap::parser::matches::arg_matches::ArgMatches` is defined in crate `clap`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/parser/matches/arg_matches.rs:66:1
    |
66  | pub struct ArgMatches {
    | ^^^^^^^^^^^^^^^^^^^^^
    = note: perhaps two different versions of crate `clap` are being used?
note: function defined here
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/bird_tool_utils-282ffc890cc6dc83/076cff1/src/clap_utils.rs:15:8
    |
15  | pub fn set_log_level(matches: &clap::ArgMatches, is_last: bool, program_name: &str, version: &str) {
    |        ^^^^^^^^^^^^^

error[E0308]: mismatched types
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:334:9
    |
333 |     bird_tool_utils::clap_utils::print_full_help_if_needed(
    |     ------------------------------------------------------ arguments to this function are incorrect
334 |         &m,
    |         ^^ expected struct `ArgMatches`, found `&ArgMatches`
    |
    = note: expected reference `&clap::parser::matches::arg_matches::ArgMatches`
               found reference `&&ArgMatches`
note: function defined here
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/bird_tool_utils-282ffc890cc6dc83/076cff1/src/clap_utils.rs:41:8
    |
41  | pub fn print_full_help_if_needed(m: &clap::ArgMatches, manual: Manual) {
    |        ^^^^^^^^^^^^^^^^^^^^^^^^^

error[E0308]: mismatched types
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:344:76
    |
338 |     let num_threads: usize = m.value_of_t("threads").unwrap();
    |                              - here the type of `m` is inferred to be `&ArgMatches`
...
344 |     let genome_fasta_files: Vec<String> = parse_list_of_genome_fasta_files(m, true).unwrap();
    |                                           -------------------------------- ^ expected struct `clap::parser::matches::arg_matches::ArgMatches`, found struct `ArgMatches`
    |                                           |
    |                                           arguments to this function are incorrect
    |
    = note: struct `ArgMatches` and struct `clap::parser::matches::arg_matches::ArgMatches` have similar names, but are actually distinct types
note: struct `ArgMatches` is defined in crate `clap`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-3.2.23/src/parser/matches/arg_matches.rs:68:1
    |
68  | pub struct ArgMatches {
    | ^^^^^^^^^^^^^^^^^^^^^
note: struct `clap::parser::matches::arg_matches::ArgMatches` is defined in crate `clap`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/parser/matches/arg_matches.rs:66:1
    |
66  | pub struct ArgMatches {
    | ^^^^^^^^^^^^^^^^^^^^^
    = note: perhaps two different versions of crate `clap` are being used?
note: function defined here
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/bird_tool_utils-282ffc890cc6dc83/076cff1/src/clap_utils.rs:52:8
    |
52  | pub fn parse_list_of_genome_fasta_files(
    |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

error[E0308]: mismatched types
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:926:59
    |
926 |     let mut cluster_subcommand = add_clap_verbosity_flags(Command::new("cluster"))
    |                                  ------------------------ ^^^^^^^^^^^^^^^^^^^^^^^ expected struct `Command`, found struct `App`
    |                                  |
    |                                  arguments to this function are incorrect
    |
note: function defined here
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/bird_tool_utils-282ffc890cc6dc83/076cff1/src/clap_utils.rs:211:8
    |
211 | pub fn add_clap_verbosity_flags(cmd: clap::Command) -> clap::Command {
    |        ^^^^^^^^^^^^^^^^^^^^^^^^

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:929:14
    |
929 |         .arg(Arg::new("full-help").long("full-help"))
    |          --- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |          |
    |          required by a bound introduced by this call
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:930:14
    |
930 |         .arg(Arg::new("full-help-roff").long("full-help-roff"))
    |          --- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |          |
    |          required by a bound introduced by this call
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:931:14
    |
931 |           .arg(Arg::new(&*GALAH_COMMAND_DEFINITION.dereplication_ani_argument)
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
932 | |             .long("ani")
933 | |             .help("Average nucleotide identity threshold for clustering")
934 | |             .takes_value(true)
935 | |             .default_value(crate::DEFAULT_ANI))
    | |______________________________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:936:14
    |
936 |           .arg(Arg::new(&*GALAH_COMMAND_DEFINITION.dereplication_fraglen_argument)
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
937 | |             .long(&*GALAH_COMMAND_DEFINITION.dereplication_fraglen_argument)
938 | |             .help("Length of fragment used in FastANI calculation (i.e. --fragLen)")
939 | |             .takes_value(true)
940 | |             .default_value(crate::DEFAULT_FRAGMENT_LENGTH))
    | |__________________________________________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:941:14
    |
941 |           .arg(Arg::new(&*GALAH_COMMAND_DEFINITION.dereplication_aligned_fraction_argument)
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
942 | |             .long("min-aligned-fraction")
943 | |             .help("Min aligned fraction of two genomes for clustering")
944 | |             .takes_value(true)
945 | |             .default_value(crate::DEFAULT_ALIGNED_FRACTION))
    | |___________________________________________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:946:14
    |
946 |           .arg(Arg::new("checkm-tab-table")
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
947 | |             .long("checkm-tab-table")
948 | |             .help("Output of CheckM lineage_wf/taxonomy_wf/qa with --tab_table specified")
949 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:950:14
    |
950 |           .arg(Arg::new("genome-info")
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
951 | |             .long("genome-info")
952 | |             .help("genomeInfo file in same format as dRep i.e. a CSV with three header columns, first line 'genome,completeness,contamination'.")
953 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:954:14
    |
954 |           .arg(Arg::new("min-completeness")
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
955 | |             .long("min-completeness")
956 | |             .help("Genomes with less than this percentage of completeness are excluded")
957 | |             .takes_value(true)
958 | |             .default_value("0"))
    | |_______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:959:14
    |
959 |           .arg(Arg::new("max-contamination")
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
960 | |             .long("max-contamination")
961 | |             .help("Genomes with greater than this percentage of contamination are excluded")
962 | |             .default_value("100")
963 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:964:14
    |
964 |           .arg(Arg::new(&*GALAH_COMMAND_DEFINITION.dereplication_quality_formula_argument)
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
965 | |             .long("quality-formula")
966 | |             .possible_values(&[
967 | |                 "completeness-4contamination",
...   |
971 | |             .default_value(crate::DEFAULT_QUALITY_FORMULA)
972 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:973:14
    |
973 |           .arg(Arg::new(&*GALAH_COMMAND_DEFINITION.dereplication_prethreshold_ani_argument)
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
974 | |             .long("precluster-ani")
975 | |             .takes_value(true)
976 | |             .default_value(crate::DEFAULT_PRETHRESHOLD_ANI))
    | |___________________________________________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:977:14
    |
977 |           .arg(Arg::new(&*GALAH_COMMAND_DEFINITION.dereplication_precluster_method_argument)
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
978 | |             .long("precluster-method")
979 | |             .help("method of calculating rough ANI. 'dashing' for HyperLogLog, 'finch' for finch MinHash")
980 | |             .possible_values(&["dashing","finch"])
981 | |             .default_value(crate::DEFAULT_PRECLUSTER_METHOD)
982 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:983:14
    |
983 |           .arg(Arg::new("threads")
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
984 | |             .short('t')
985 | |             .long("threads")
986 | |             .help("Number of CPU threads to use")
987 | |             .default_value("1")
988 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
   --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:989:14
    |
989 |           .arg(Arg::new("output-cluster-definition")
    |  __________---_^
    | |          |
    | |          required by a bound introduced by this call
990 | |             .short('o')
991 | |             .long("output-cluster-definition")
992 | |             .help("Output a file of representative<TAB>member lines")
...   |
998 | |                 "full-help-roff",])
999 | |             .takes_value(true))
    | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
    |
    = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
    = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
   --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
    |
165 |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
    |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
    --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:1000:14
     |
1000 |           .arg(Arg::new("output-representative-fasta-directory")
     |  __________---_^
     | |          |
     | |          required by a bound introduced by this call
1001 | |             .long("output-representative-fasta-directory")
1002 | |             .help("Symlink representative genomes into this directory")
1003 | |             .required_unless_present_any(&[
...    |
1008 | |                 "full-help-roff",])
1009 | |             .takes_value(true))
     | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
     |
     = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
     = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
    --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
     |
165  |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
     |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
    --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:1010:14
     |
1010 |           .arg(Arg::new("output-representative-fasta-directory-copy")
     |  __________---_^
     | |          |
     | |          required by a bound introduced by this call
1011 | |             .long("output-representative-fasta-directory-copy")
1012 | |             .help("Copy representative genomes into this directory")
1013 | |             .required_unless_present_any(&[
...    |
1018 | |                 "full-help-roff",])
1019 | |             .takes_value(true))
     | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
     |
     = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
     = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
    --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
     |
165  |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
     |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `clap::builder::arg::Arg: From<clap::Arg<'_>>` is not satisfied
    --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:1020:14
     |
1020 |           .arg(Arg::new("output-representative-list")
     |  __________---_^
     | |          |
     | |          required by a bound introduced by this call
1021 | |             .long("output-representative-list")
1022 | |             .help("Print newline separated list of paths to representatives into this directory")
1023 | |             .required_unless_present_any(&[
...    |
1028 | |                 "full-help-roff",])
1029 | |             .takes_value(true));
     | |______________________________^ the trait `From<clap::Arg<'_>>` is not implemented for `clap::builder::arg::Arg`
     |
     = help: the trait `From<&clap::builder::arg::Arg>` is implemented for `clap::builder::arg::Arg`
     = note: required for `clap::Arg<'_>` to implement `Into<clap::builder::arg::Arg>`
note: required by a bound in `clap::builder::command::Command::arg`
    --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-4.1.4/src/builder/command.rs:165:34
     |
165  |     pub fn arg(mut self, a: impl Into<Arg>) -> Self {
     |                                  ^^^^^^^^^ required by this bound in `Command::arg`

error[E0277]: the trait bound `App<'_>: From<clap::builder::command::Command>` is not satisfied
    --> /storage/home/hcoda1/6/rridley3/.cargo/git/checkouts/galah-65775e8f2cbe6db4/68e920b/src/cluster_argument_parsing.rs:1034:27
     |
1034 |     return app.subcommand(cluster_subcommand);
     |                ---------- ^^^^^^^^^^^^^^^^^^ the trait `From<clap::builder::command::Command>` is not implemented for `App<'_>`
     |                |
     |                required by a bound introduced by this call
     |
     = note: required for `clap::builder::command::Command` to implement `Into<App<'_>>`
note: required by a bound in `App::<'help>::subcommand`
    --> /storage/home/hcoda1/6/rridley3/.cargo/registry/src/github.com-1ecc6299db9ec823/clap-3.2.23/src/builder/command.rs:415:26
     |
415  |     pub fn subcommand<S: Into<App<'help>>>(mut self, subcmd: S) -> Self {
     |                          ^^^^^^^^^^^^^^^^ required by this bound in `App::<'help>::subcommand`

Some errors have detailed explanations: E0277, E0308.
For more information about an error, try `rustc --explain E0277`.
error: could not compile `galah` due to 22 previous errors