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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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Error during installation #180

Closed molecule53 closed 1 month ago

molecule53 commented 1 month ago

Hello,

I run: git clone https://github.com/nanoporetech/modkit.git cd modkit

After, I am running cargo install --path . but I am getting the error bellow:

running cd "/Data1/modkit/target/release/build/openssl-sys-fc6a0e7de0c255d6/out/openssl-build/build/src" && "make" "depend"

--- stderr thread 'main' panicked at /home/ubuntu/.cargo/registry/src/index.crates.io-6f17d22bba15001f/openssl-src-300.2.3+3.2.1/src/lib.rs:611:9:

Error building OpenSSL dependencies: Command: cd "/Data1/modkit/target/release/build/openssl-sys-fc6a0e7de0c255d6/out/openssl-build/build/src" && "make" "depend" Failed to execute: No such file or directory (os error 2)

note: run with RUST_BACKTRACE=1 environment variable to display a backtrace warning: build failed, waiting for other jobs to finish... error: failed to compile mod_kit v0.2.8 (/Data1/modkit), intermediate artifacts can be found at /Data1/modkit/target. To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path.

Thank you!

ArtRand commented 1 month ago

Hello @molecule53,

Could you tell me about the operating system and environment you're installing into? It looks like Open SSL is failing to build. From the error, it looks like your system doesn't have make, could you check if that's the case? The dependencies of modkit require CMAKE as well, so you might want to install that once you have a chance.

molecule53 commented 1 month ago

Hello and Thank you!

Installing CMAKE helped!

I was able to run modkit.

I have a couple of questions:

1. I run /home/ubuntu/.cargo/bin/modkit pileup /Data1/dorado_output.sorted.bam /Data1/dorado_modkit_pileup_CpG.bed --cpg --ref /Data1/genome_reference.fasta --ignore h --combine-strands

           In the 4th column of the .bed file I got not only modification code m but also modification      code a. Is it something expected or am I missing something? I am interested in mC.

    2) Is there any way to look at mC in CHH and CHG (H is anybase but G)?

Thank you!

    

From: Arthur Rand @.> Sent: Monday, May 6, 2024 2:58 PM To: nanoporetech/modkit @.> Cc: McKinlay, Anastasia @.>; Mention @.> Subject: [External] Re: [nanoporetech/modkit] Error during installation (Issue #180)

This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hello @molecule53https://github.com/molecule53,

Could you tell me about the operating system and environment you're installing into? It looks like Open SSL is failing to build. From the error, it looks like your system doesn't have make, could you check if that's the case? The dependencies of modkit require CMAKE as well, so you might want to install that once you have a chance.

— Reply to this email directly, view it on GitHubhttps://github.com/nanoporetech/modkit/issues/180#issuecomment-2096704302, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A6WBDROGAYE5MJFELCHOMULZA7HG7AVCNFSM6AAAAABHJQ434OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJWG4YDIMZQGI. You are receiving this because you were mentioned.

ArtRand commented 1 month ago

Hello @molecule53

If you performed basecalling and modification calling with a 6mA and 5mC model (sounds like you did) then you'll get a base modification call at all Cs and As in each read. What can happen is, if a read has a C-to-A alignment mismatch you'll still get a 6mA canonical/modified call at that site (even though it's a reference C). It's usually clear this is the case because the valid coverage will be much lower than the median for the run. If you only care about 5mC, you can filter out the records with a in the mod-code column.

If you want to look at CpG, CHH, and CHG, you can use the --motif option, the documentation is on github.

molecule53 commented 1 month ago

Hello,

Thank you! I did see --motif option. I am not sure if can I look at CHH or CHG using one line of code (H can be either A, T, or C). Any suggestions?

Best, Anastasia

From: Arthur Rand @.> Sent: Friday, May 10, 2024 6:06 PM To: nanoporetech/modkit @.> Cc: McKinlay, Anastasia @.>; Mention @.> Subject: [External] Re: [nanoporetech/modkit] Error during installation (Issue #180)

This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hello @molecule53https://github.com/molecule53

If you performed basecalling and modification calling with a 6mA and 5mC model (sounds like you did) then you'll get a base modification call at all Cs and As in each read. What can happen is, if a read has a C-to-A alignment mismatch you'll still get a 6mA canonical/modified call at that site (even though it's a reference C). It's usually clear this is the case because the valid coverage will be much lower than the median for the run. If you only care about 5mC, you can filter out the records with a in the mod-code column.

If you want to look at CpG, CHH, and CHG, you can use the --motif option, the documentationhttps://nanoporetech.github.io/modkit/intro_bedmethyl.html#narrowing-output-to-specific-motifs is on github.

— Reply to this email directly, view it on GitHubhttps://github.com/nanoporetech/modkit/issues/180#issuecomment-2105325241, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A6WBDRMCSG6UXG3HNYABXWLZBVAHNAVCNFSM6AAAAABHJQ434OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBVGMZDKMRUGE. You are receiving this because you were mentioned.Message ID: @.***>

ArtRand commented 1 month ago

Hello @molecule53,

Sorry for the slow reply. You can use --motif CHH 0 --motif CHG 0 the parser in modkit understands iupac codes.

molecule53 commented 1 month ago

Thank you!

From: Arthur Rand @.> Sent: Monday, May 20, 2024 11:22 AM To: nanoporetech/modkit @.> Cc: McKinlay, Anastasia @.>; Mention @.> Subject: [External] Re: [nanoporetech/modkit] Error during installation (Issue #180)

This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hello @molecule53https://github.com/molecule53,

Sorry for the slow reply. You can use --motif CHH 0 --motif CHG 0 the parser in modkit understands iupachttps://www.bioinformatics.org/sms/iupac.html codes.

— Reply to this email directly, view it on GitHubhttps://github.com/nanoporetech/modkit/issues/180#issuecomment-2120680059, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A6WBDRKNXGWJVJTDAHTUBVDZDIINHAVCNFSM6AAAAABHJQ434OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRQGY4DAMBVHE. You are receiving this because you were mentioned.Message ID: @.***>

ArtRand commented 1 month ago

Great, let me know if you have any more questions.