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JTK -- a regional diploid genome assembler

License: MIT License

Rust 98.03% Shell 1.36% R 0.59% Awk 0.02%

bioinfomatics genome-assembly

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yoshihikosuzuki

jtk's Issues

General Inquiry

Hello,

I appreciate the excellent program you've provided.

I have a couple of quick questions:

Multiple input reads: Can I utilize both PacBio HiFi and ONT Ultra-long reads simultaneously?
Multiple regions and assemblies: Is it possible to use the program for multiple regions across different assemblies? For example, Chromosome 1 (10 Mb regions), Chromosome 2 (10 Mb regions), and Chromosome 3 (10 Mb regions). Or should I submit individual jobs for each chromosomal region?

Any suggestions you can provide would be greatly appreciated.

Regards,

Taek

GFA2 visualization

Thanks for the exciting new development! Any recommendations on visualizing the answer? Or maybe producing a GFA1 output as an option?

Convert GFA to phased assembly

Hi there

Could you please let me know how to convert the GFA result to phased fasta?

Thanks

Some issues with the latest versions of Rust

Hello

It looks like the latest version of Rust is causing some issues when compiling jtk.

With the latest version of Rust (1.70.0) I'm getting this error:

error[E0554]: `#![feature]` may not be used on the stable release channel
 --> haplotyper/src/lib.rs:1:12
  |
1 | #![feature(is_sorted)]
  |            ^^^^^^^^^

When I install the latest nightly build (1.72.0-nightly), I get this error:

error[E0635]: unknown feature `proc_macro_span_shrink`
  --> /home/harald/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proc-macro2-1.0.51/src/lib.rs:92:30
   |
92 |     feature(proc_macro_span, proc_macro_span_shrink)
   |                              ^^^^^^^^^^^^^^^^^^^^^^

After looking for different nightly builds, I found that installing 1.68.0-nightly made it compile, so possibly the documentation needs to be updated.

jtk build failed

After installing cargo ( 1.72.1 (103a7ff2e 2023-08-15)) and minimap2 (2.26-r1175) I have attempted installing JTK using the guide.
When running cargo build --release, as well as cargo check && cargo build --release, both produce the same warning:

warning: build failed, waiting for other jobs to finish...

which is preceded by this error:

error occurred: Command "c++" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-gdwarf-4" "-fno-omit-frame-pointer" "-m64" "-I" "src/edlib/include" "-Wall" "-Wextra" "-Wall" "-Wextra" "-O3" "-g" "-o" "/net/fs-2/scale/OrionStore/ScratchProjects/Transpose/doja/jtk/target/debug/build/edlib_sys-b0ee97c476634a05/out/src/edlib/src/edlib.o" "-c" "src/edlib/src/edlib.cpp" with args "c++" did not execute successfully (status code exit status: 1).

Would greatly appreciate any help

Can not install JTK

Hi there

My cargo version is 1.73.0.

I used "cargo +nightly build --release" to install JTK and got an error below

Compiling jtk_cli v0.1.0 (/mnt/chsrhome/xxx/src/jtk/cli)
error: linking with `cc` failed: exit status: 1
  |
  = note: LC_ALL="C" PATH="/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/xxx/.cargo/bin:/home/xxx/miniconda3/bin:/home/xxx/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/xxx/src/princess:/mnt/chsrhome/xxx/.local/bin:/mnt/chsrhome/xxx/.local/bin" VSLANG="1033" "cc" "-m64" "/tmp/rustckv1hKH/symbols.o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb.gen_sim_genome_segdup.f10d61189ced6ac9-cgu.0.rcgu.o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb.gen_sim_genome_segdup.f10d61189ced6ac9-cgu.1.rcgu.o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb.gen_sim_genome_segdup.f10d61189ced6ac9-cgu.2.rcgu.o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb.gen_sim_genome_segdup.f10d61189ced6ac9-cgu.3.rcgu.o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb.gen_sim_genome_segdup.f10d61189ced6ac9-cgu.4.rcgu.o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb.52dlul921kpsqclq.rcgu.o" "-Wl,--as-needed" "-L" "/mnt/chsrhome/xxx/src/jtk/target/release/deps" "-L" "/mnt/chsrhome/xxx/src/jtk/target/release/build/edlib_sys-53dd7691be74d259/out" "-L" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/librand_xoshiro-9d1bd639a4b2d11f.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libkiley-4afcb6c588d8c622.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libedlib_sys-932ab1349154f8b1.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libbio_utils-7f2887f8736760ae.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libbytecount-a6c3c9705795b477.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libserde-6a76e096f3e36f13.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/librayon-b17bef6baa313287.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/librayon_core-324d0239257b5ee1.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libnum_cpus-4b3871561d843ade.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libcrossbeam_deque-41adb3a8d1c9699a.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libcrossbeam_epoch-9c4114931f6a8b14.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libmemoffset-4ad551629c429fb6.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libscopeguard-9480aa1ac9ac9b8e.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libcrossbeam_channel-e96fa869d4cab4b0.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libcrossbeam_utils-1eb759b97c2f998f.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libeither-78605f00e8342a46.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/librand-89fe3d3cca8600a3.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/librand_chacha-4702648f9bf75c0e.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libppv_lite86-e126acff3847d4dd.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/librand_core-dcbbc2aa633f6568.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libgetrandom-d6e870a2ed2cb594.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/liblibc-f7ab123bf25e2fea.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/libcfg_if-c3c8e42c08821148.rlib" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/liblog-c813e2bb71f6d743.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d787e53a290411e2.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-d772252209e2742b.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-6ecdf1ea0ff6e093.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libmemchr-6fe0fbbff7f67836.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-9b8c277eaa19322c.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-6f650d56687f361f.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-46dd15171ac21d07.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd_detect-fb22c0b7181dff10.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-fee0e81d645c26e5.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-12b62e8197e1fe1e.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-f19ca64f1728e7dd.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-2849ed8ae5c8b127.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-686cf0e89dd87a14.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-f412a4d0fdbc296b.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-ff4ae84067796be3.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-a4e81b6d6bd074c0.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-cd2f2bc505f56f50.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-ec02dd343723da85.rlib" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-5ae5f870b7d1798c.rlib" "-Wl,-Bdynamic" "-lstdc++" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/mnt/chsrhome/xxx/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/mnt/chsrhome/xxx/src/jtk/target/release/deps/gen_sim_genome_segdup-e1a9d5ae874731bb" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,-O1" "-nodefaultlibs"
  = note: /usr/bin/ld: /mnt/chsrhome/xxx/src/jtk/target/release/deps/libedlib_sys-932ab1349154f8b1.rlib(edlib.o): unable to initialize decompress status for section .debug_info
          /usr/bin/ld: /mnt/chsrhome/xxx/src/jtk/target/release/deps/libedlib_sys-932ab1349154f8b1.rlib(edlib.o): unable to initialize decompress status for section .debug_info
          /mnt/chsrhome/xxx/src/jtk/target/release/deps/libedlib_sys-932ab1349154f8b1.rlib: error adding symbols: File format not recognized
          collect2: error: ld returned 1 exit status

Any suggestions are appreciated.

haplotyper error

Hello! Good afternoon. Good work developing the program.
I have managed to download, install and run the program successfully with the example reads, however, when I try to run my nanopore reads I get this consistent error message in the log file:

[2023-10-30T17:39:17Z DEBUG jtk_cli::pipeline] Opening C1_candida_trial_jtk.fq
[2023-10-30T17:39:21Z DEBUG haplotyper::entry] Input    ReadNum 37102
[2023-10-30T17:39:21Z DEBUG haplotyper::entry] Input    BasePair(Mbp)   386
[2023-10-30T17:39:45Z DEBUG haplotyper::repeat_masking] MASKREPEAT      UNIQUE  0       6219258
[2023-10-30T17:39:45Z DEBUG haplotyper::repeat_masking] MASKREPEAT      MaskMoreThan    1540    12
[2023-10-30T17:39:45Z DEBUG haplotyper::repeat_masking] MASKREPEAT      MaskLen 12      6208
[2023-10-30T17:39:46Z DEBUG haplotyper::repeat_masking] MASKREPEAT      TotalMask       60302166        386122434
[2023-10-30T17:39:46Z DEBUG haplotyper::repeat_masking] MASKREPEAT      MaskedKmers     6208    12
[2023-10-30T17:39:46Z DEBUG haplotyper::determine_chunks] MINIMAP2      VERSION 2.26-r1175

[2023-10-30T17:39:46Z DEBUG haplotyper::determine_chunks] Select Unit: Configuration:DetermineUnitConfig { chunk_len: 2000, chunk_num: 3000
, margin: 500, threads: 8, min_cluster: 2, exclude_repeats: 0.85, purge_copy_num: 8, seed: 19090432890 }
[2023-10-30T17:40:12Z DEBUG haplotyper::determine_chunks] UNITNUM       3000    PICKED
[2023-10-30T17:40:12Z DEBUG haplotyper::determine_chunks] DETERMINE     UnitOvlp        Creating        "/shared/home/sv264/git_repos/tools
/seq_tools/assemblers/jtk/52515411"
[2023-10-30T17:40:13Z DEBUG haplotyper::determine_chunks] DETERMINE     UnitOvlp        Removing        "/shared/home/sv264/git_repos/tools
/seq_tools/assemblers/jtk/52515411"
[2023-10-30T17:40:14Z DEBUG haplotyper::determine_chunks] UNITNUM       1679    REMOVED
[2023-10-30T17:40:14Z DEBUG haplotyper::encode] ENCODE  ErrorRate       0.3
[2023-10-30T17:40:14Z DEBUG haplotyper::encode] Creating "/shared/home/sv264/git_repos/tools/seq_tools/assemblers/jtk/97736991".
[2023-10-30T17:40:41Z DEBUG haplotyper::encode] Removing "/shared/home/sv264/git_repos/tools/seq_tools/assemblers/jtk/97736991"
thread '<unnamed>' panicked at 'range end index 24500 out of range for slice of length 10966', haplotyper/src/encode/mod.rs:141:23
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
thread '<unnamed>' panicked at 'range end index 18579 out of range for slice of length 2257', haplotyper/src/encode/mod.rs:141:23
thread '<unnamed>' panicked at 'range end index 3736 out of range for slice of length 0', haplotyper/src/encode/mod.rs:141:23
thread '<unnamed>' panicked at 'range end index 3836 out of range for slice of length 1696', haplotyper/src/encode/mod.rs:148:42
thread '<unnamed>' panicked at 'range end index 6594 out of range for slice of length 501', haplotyper/src/encode/mod.rs:141:23

and goes one for a while.
Any idea if this has happened before or on how to fix this?

Thanks!
Sam :D

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