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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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Issue with odgi #139

Closed viannam closed 2 years ago

viannam commented 3 years ago

Hello all,

I am having an error with the pggb/0.1.3. in the smoothxg phase. Apparently could not find flag 'O' in odgi build options:

warning [libhandlegraph]: Serialized object does not appear to match deserialzation type.
warning [libhandlegraph]: It is either an old version or in the wrong format.
warning [libhandlegraph]: Attempting to load it anyway. Future releases will reject it!
terminate called after throwing an instance of 'std::runtime_error'
 what():  Error rewinding to load non-magic-prefixed "SerializableHandleGraph"

This is the command line: pggb -i test.fa -s1000 -n10 -p90 -U -v -L -S -V -o /PGGB

input file: test.txt output file: pggb_test_9105756out.txt

Thank you in advance.

subwaystation commented 3 years ago

Hi @viannam For me the following worked with the most recent 0.2.0 release: pggb -i test_viannam.fa -s1000 -n10 -p90 -U -v -L -S -o /home/heumos/Downloads/viannam_pggb Could you please update and try again? Also the option -V requires an argument. If you don't specify that, PGGB will think the input for -V is -o /PGGB and you will run into troubles downstream. Thanks!

ekg commented 3 years ago

That's not been merged get. https://github.com/pangenome/pggb/pull/138

I expect to merge in the next few days. Until then, you'll want to checkout the branch in that PR and build the docker image using its Dockerfile.

wendelljpereira commented 2 years ago

Dear authors,

Thank you very much for developing this software!

I tried to build the docker image using the branch v0.2-pre-release but received an error. Could you check if there is a problem?

I executed the following command (in a MAC OS):

docker build https://github.com/pangenome/pggb.git\#v0.2-pre-release

This is the part of the output that contains the error message:

`ERROR [ 8/12] RUN git clone https://github.com/marschall-lab/GFAffix.git && cd GFAffix && git pull && git checkout b75302b 79.1s

[ 8/12] RUN git clone https://github.com/marschall-lab/GFAffix.git && cd GFAffix && git pull && git checkout b75302b && cargo install --force --path . && mv /root/.cargo/bin/gfaffix /usr/local/bin/gfaffix:

11 0.279 Cloning into 'GFAffix'...

11 1.080 hint: Pulling without specifying how to reconcile divergent branches is

11 1.080 hint: discouraged. You can squelch this message by running one of the following

11 1.080 hint: commands sometime before your next pull:

11 1.080 hint:

11 1.080 hint: git config pull.rebase false # merge (the default strategy)

11 1.080 hint: git config pull.rebase true # rebase

11 1.080 hint: git config pull.ff only # fast-forward only

11 1.080 hint:

11 1.080 hint: You can replace "git config" with "git config --global" to set a default

11 1.080 hint: preference for all repositories. You can also pass --rebase, --no-rebase,

11 1.080 hint: or --ff-only on the command line to override the configured default per

11 1.080 hint: invocation.

11 1.463 Already up to date.

11 1.468 Note: switching to 'b75302b'.

11 1.468

11 1.468 You are in 'detached HEAD' state. You can look around, make experimental

11 1.468 changes and commit them, and you can discard any commits you make in this

11 1.468 state without impacting any branches by switching back to a branch.

11 1.468

11 1.468 If you want to create a new branch to retain commits you create, you may

11 1.468 do so (now or later) by using -c with the switch command. Example:

11 1.468

11 1.468 git switch -c

11 1.468

11 1.468 Or undo this operation with:

11 1.468

11 1.468 git switch -

11 1.468

11 1.468 Turn off this advice by setting config variable advice.detachedHead to false

11 1.468

11 1.468 HEAD is now at b75302b switched back to cargo maintained rs-handlegraph version after critical bugfix has been released

11 1.644 Installing gfaffix v0.1.2 (/GFAffix)

11 1.942 Updating crates.io index

11 27.17 Downloading crates ...

11 28.22 Downloaded proc-macro-error v1.0.4

11 28.22 Downloaded proc-macro-error-attr v1.0.4

11 28.23 Downloaded env_logger v0.7.1

11 28.26 Downloaded quick-error v1.2.3

11 28.35 Downloaded handlegraph v0.7.0-alpha.9

11 28.39 Downloaded quick-csv v0.1.6

11 28.49 Downloaded version_check v0.9.3

11 28.50 Downloaded lazy_static v1.4.0

11 28.51 Downloaded regex-automata v0.1.10

11 28.52 Downloaded num_cpus v1.13.0

11 28.52 Downloaded rand_core v0.6.3

11 28.53 Downloaded num-traits v0.2.14

11 28.53 Downloaded termcolor v1.1.2

11 28.53 Downloaded strsim v0.10.0

11 28.54 Downloaded rustc-hash v1.1.0

11 28.54 Downloaded atty v0.2.14

11 28.54 Downloaded textwrap v0.14.2

11 28.54 Downloaded rayon v1.5.1

11 28.56 Downloaded memchr v2.4.1

11 28.56 Downloaded aho-corasick v0.7.18

11 28.57 Downloaded log v0.4.14

11 28.57 Downloaded crossbeam-epoch v0.9.5

11 28.58 Downloaded scopeguard v1.1.0

11 28.58 Downloaded clap_derive v3.0.0-beta.5

11 28.58 Downloaded proc-macro2 v1.0.30

11 28.59 Downloaded fnv v1.0.7

11 28.59 Downloaded bitflags v1.3.2

11 28.59 Downloaded ryu v1.0.5

11 28.60 Downloaded unicase v2.6.0

11 28.60 Downloaded bytemuck v1.7.2

11 28.61 Downloaded quote v1.0.10

11 28.62 Downloaded indexmap v1.7.0

11 28.62 Downloaded hashbrown v0.11.2

11 28.63 Downloaded rayon-core v1.9.1

11 28.64 Downloaded cfg-if v1.0.0

11 28.64 Downloaded either v1.6.1

11 28.64 Downloaded crossbeam-utils v0.8.5

11 28.64 Downloaded unicode-segmentation v1.8.0

11 28.65 Downloaded crossbeam-deque v0.8.1

11 28.65 Downloaded heck v0.3.3

11 28.65 Downloaded unicode-width v0.1.9

11 28.73 Downloaded clap v3.0.0-beta.5

11 28.76 Downloaded regex v1.5.4

11 28.78 Downloaded nom v5.1.2

11 28.82 Downloaded bytemuck_derive v1.0.1

11 28.83 Downloaded wyhash v0.5.0

11 28.83 Downloaded humantime v1.3.0

11 28.83 Downloaded succinct v0.5.2

11 28.84 Downloaded memmap v0.7.0

11 28.84 Downloaded boomphf v0.5.9

11 28.84 Downloaded regex-syntax v0.6.25

11 28.85 Downloaded unicode-xid v0.2.2

11 28.86 Downloaded memoffset v0.6.4

11 28.86 Downloaded anyhow v1.0.44

11 28.86 Downloaded rustc-serialize v0.3.24

11 28.87 Downloaded os_str_bytes v4.2.0

11 28.88 Downloaded syn v1.0.80

11 28.91 Downloaded lexical-core v0.7.6

11 28.93 Downloaded bstr v0.2.17

11 28.94 Downloaded autocfg v1.0.1

11 28.95 Downloaded static_assertions v1.1.0

11 28.95 Downloaded libc v0.2.104

11 28.99 Downloaded crossbeam-channel v0.5.1

11 28.99 Downloaded byteorder v1.4.3

11 29.00 Downloaded arrayvec v0.5.2

11 29.06 Downloaded gfa v0.10.0

11 29.19 Compiling autocfg v1.0.1

11 29.19 Compiling version_check v0.9.3

11 29.19 Compiling cfg-if v1.0.0

11 29.19 Compiling libc v0.2.104

11 29.19 Compiling proc-macro2 v1.0.30

11 29.20 Compiling unicode-xid v0.2.2

11 29.36 Compiling lazy_static v1.4.0

11 29.45 Compiling memchr v2.4.1

11 29.59 Compiling crossbeam-utils v0.8.5

11 29.90 Compiling syn v1.0.80

11 29.95 Compiling crossbeam-epoch v0.9.5

11 30.03 Compiling ryu v1.0.5

11 30.05 Compiling scopeguard v1.1.0

11 30.11 Compiling rayon-core v1.9.1

11 30.18 Compiling lexical-core v0.7.6

11 30.25 Compiling log v0.4.14

11 30.44 Compiling bitflags v1.3.2

11 30.57 Compiling regex-syntax v0.6.25

11 30.62 Compiling anyhow v1.0.44

11 30.66 Compiling arrayvec v0.5.2

11 30.73 Compiling static_assertions v1.1.0

11 30.74 Compiling rand_core v0.6.3

11 30.76 Compiling either v1.6.1

11 30.91 Compiling unicode-segmentation v1.8.0

11 31.02 Compiling regex-automata v0.1.10

11 31.13 Compiling unicode-width v0.1.9

11 31.30 Compiling fnv v1.0.7

11 31.36 Compiling quick-error v1.2.3

11 31.36 Compiling termcolor v1.1.2

11 31.49 Compiling hashbrown v0.11.2

11 31.56 Compiling byteorder v1.4.3

11 31.65 Compiling rustc-serialize v0.3.24

11 31.85 Compiling strsim v0.10.0

11 32.12 Compiling rustc-hash v1.1.0

11 32.53 Compiling proc-macro-error-attr v1.0.4

11 32.58 Compiling nom v5.1.2

11 33.04 Compiling proc-macro-error v1.0.4

11 33.04 Compiling unicase v2.6.0

11 33.11 Compiling memoffset v0.6.4

11 33.55 Compiling rayon v1.5.1

11 33.57 Compiling num-traits v0.2.14

11 33.63 Compiling indexmap v1.7.0

11 34.15 Compiling wyhash v0.5.0

11 34.27 Compiling textwrap v0.14.2

11 34.60 Compiling humantime v1.3.0

11 34.72 Compiling heck v0.3.3

11 39.75 Compiling quick-csv v0.1.6

11 39.94 Compiling num_cpus v1.13.0

11 40.41 Compiling atty v0.2.14

11 40.65 Compiling memmap v0.7.0

11 40.91 Compiling quote v1.0.10

11 41.48 Compiling aho-corasick v0.7.18

11 41.49 Compiling bstr v0.2.17

11 41.59 Compiling os_str_bytes v4.2.0

11 42.12 Compiling crossbeam-channel v0.5.1

11 45.63 Compiling regex v1.5.4

11 46.27 Compiling succinct v0.5.2

11 46.88 Compiling crossbeam-deque v0.8.1

11 47.78 Compiling env_logger v0.7.1

11 54.56 Compiling bytemuck_derive v1.0.1

11 54.94 Compiling clap_derive v3.0.0-beta.5

11 56.44 Compiling bytemuck v1.7.2

11 56.58 Compiling boomphf v0.5.9

11 56.84 Compiling gfa v0.10.0

11 58.53 Compiling handlegraph v0.7.0-alpha.9

11 59.61 Compiling clap v3.0.0-beta.5

11 78.27 Compiling gfaffix v0.1.2 (/GFAffix)

11 78.39 error[E0432]: unresolved import clap::Clap

11 78.39 --> src/main.rs:11:5

11 78.39 |

11 78.39 11 | use clap::Clap;

11 78.39 | ^^^^^^^^^^ no Clap in the root

11 78.39

11 78.39 error[E0433]: failed to resolve: could not find Clap in clap

11 78.39 --> src/main.rs:27:16

11 78.39 |

11 78.39 27 | #[derive(clap::Clap, Debug)]

11 78.39 | ^^^^ could not find Clap in clap

11 78.39

11 78.41 error: cannot find attribute clap in this scope

11 78.41 --> src/main.rs:28:3

11 78.41 |

11 78.41 28 | #[clap(

11 78.41 | ^^^^

11 78.41

11 78.41 error: cannot find attribute clap in this scope

11 78.41 --> src/main.rs:36:7

11 78.41 |

11 78.41 36 | #[clap(index = 1, about = "graph in GFA1 format", required = true)]

11 78.41 | ^^^^

11 78.41

11 78.41 error: cannot find attribute clap in this scope

11 78.41 --> src/main.rs:39:7

11 78.41 |

11 78.41 39 | #[clap(

11 78.41 | ^^^^

11 78.41

11 78.41 error: cannot find attribute clap in this scope

11 78.41 --> src/main.rs:47:7

11 78.41 |

11 78.41 47 | #[clap(

11 78.41 | ^^^^

11 78.41

11 78.41 error: cannot find attribute clap in this scope

11 78.41 --> src/main.rs:55:7

11 78.41 |

11 78.41 55 | #[clap(

11 78.41 | ^^^^

11 78.41

11 78.41 error: cannot find attribute clap in this scope

11 78.41 --> src/main.rs:62:7

11 78.41 |

11 78.41 62 | #[clap(

11 78.41 | ^^^^

11 78.41

11 78.61 error[E0599]: no function or associated item named parse found for struct Command in the current scope

11 78.61 --> src/main.rs:1117:27

11 78.61 |

11 78.61 35 | pub struct Command {

11 78.61 | ------------------ function or associated item parse not found for this

11 78.61 ...

11 78.61 1117 | let params = Command::parse();

11 78.61 | ^^^^^ function or associated item not found in Command

11 78.61 |

11 78.61 = help: items from traits can only be used if the trait is implemented and in scope

11 78.61 = note: the following traits define an item parse, perhaps you need to implement one of them:

11 78.61 candidate #1: Parser

11 78.61 candidate #2: OptFields

11 78.61 candidate #3: nom::sequence::Tuple

11 78.61

11 78.63 Some errors have detailed explanations: E0432, E0433, E0599.

11 78.63 For more information about an error, try rustc --explain E0432.

11 78.66 error: failed to compile gfaffix v0.1.2 (/GFAffix), intermediate artifacts can be found at /GFAffix/target

11 78.66

11 78.66 Caused by:

11 78.66 could not compile gfaffix due to 9 previous errors

executor failed running [/bin/sh -c git clone https://github.com/marschall-lab/GFAffix.git && cd GFAffix && git pull && git checkout b75302b && cargo install --force --path . && mv /root/.cargo/bin/gfaffix /usr/local/bin/gfaffix]: exit code: 101

`

subwaystation commented 2 years ago

Hi @wendelljpereira Unfortunately, the current branch you are trying to work with has this compilation issue with GFAffix. Maybe an older rust version can be a workaround. I will take a look.

AndreaGuarracino commented 2 years ago

@wendelljpereira, I just fixed the problem. Could you please try again?

wendelljpereira commented 2 years ago

Hi @AndreaGuarracino,

The Docker image was built correctly now. Thank you very much for your help!

Best Regards, Wendell

subwaystation commented 2 years ago

:+1: