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wdecoster / chopper

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Missing libraries of chopper #8

Closed MohammadAliAmir closed 1 year ago

MohammadAliAmir commented 1 year ago

Hi @wdecoster, I installed the the binary of version 0.4.0 through chopper-linux.zip of that release. When I try to run it, it complains that there are some missing libraries required by chopper. Is that correct?

$ chopper
chopper: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by chopper)
chopper: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by chopper)
chopper: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by chopper)
chopper: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by chopper)
chopper: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by chopper)
chopper: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by chopper)
chopper: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by chopper)
chopper: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by chopper)

Can you give me all the required libraries/dependencies to use chopper?

Kind regards, Mohammad Ali Amir

wdecoster commented 1 year ago

I added another binary, could you please try the chopper-musl.zip?

MohammadAliAmir commented 1 year ago

That looks fine now, thank you for the quick response!

dodoflyy commented 1 year ago

Hell, v0.5.0 still have this problem?

$ ./chopper --help
./chopper: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by ./chopper)
./chopper: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by ./chopper)
./chopper: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by ./chopper)
wdecoster commented 1 year ago

Did you use the musl build?

dodoflyy commented 1 year ago

I used binary file downloaded from the release.

wdecoster commented 1 year ago

Yes. Did you download the musl binary from the release?

dodoflyy commented 1 year ago

ok, chopper-musl.zip works, thanks.

kaanokay commented 1 year ago

Hi,

  1. Even if I used musl binary, I got the similar error: "/lib64/libm.so.6: version `GLIBC_2.29' not found".

  2. In addition to that, installation of chopper via conda is problematic. When I tried to install it, I got following error: "Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve".

  3. There is a bug in read length filtering, it does not filter reads that have length of interest.

Btw, fastq files I'm trying to filter have MM and ML tags for methylation so they are modified fastq. I converted modified BAM files to fastq files which keep methylation info.

Bw.

mianlee commented 1 year ago
  1. got the similar

I had the same issue !