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Armin Töpfer armintoepfer @PacificBiosciences Gelsenkirchen http://www.armintoepfer.com Husband. Father. Computational biology PhD. Bioinformagician. Principal Software Engineer & Associate Director. C++ Purist. Geek. Digital Artist. Photographer.

armintoepfer/haploclique 2

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

armintoepfer/apparatus 1

Deep learning of sequencing data

armintoepfer/bam-io-throughput 1

BAM I/O Throughput Benchmark

armintoepfer/ggeyecandy 1

Various R scripts to generate appealing data visualizations

armintoepfer/BAMExtract 0

Extracts regions from a bam file and exports as in sam format

armintoepfer/bauhaus 0

minimal tertiary analysis for PacBio

armintoepfer/bioconda-recipes 0

Conda recipes for the bioconda channel.

startedPacificBiosciences/pbbioconda

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issue commentPacificBiosciences/pbbioconda

Lima terminate called without an active exception

Include the header :)

samtools view -h sample.ccs.bam | head -n 1000 | samtools -bS > test.ccs.bam
zmz1988

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issue commentPacificBiosciences/align-clr-to-ccs

If no .bam.pbi files for associated .bam files, then actc exits without outputting stderr or stdout

Thanks for the bug report. I will check and fix it.

jelber2

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issue closedPacificBiosciences/pbbioconda

zmwfilter very slow

Hi, Filtering 14,000 ZMW holes from an 800 Gb subreads BAM file using 'zmwfilter' is taking > 3 hours. That seems too slow. Is there any speed improvement, or any other way to do this?

closed time in 4 days

gevro

issue commentPacificBiosciences/pbbioconda

zmwfilter very slow

It's in bioconda. Still as version 1.0.0, though the internal version is 1.2.0. Will correct that at some point.

gevro

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push eventbioconda/bioconda-recipes

Armin Töpfer

commit sha 7ff9fcac5c8b5f26affb12dd44a04ea8fa29de21

Update PacBio `zmwfilter` 1.0.0 rebuild (#32463)

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delete branch bioconda/bioconda-recipes

delete branch : zmwfilter-1.0.0-1

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PR merged bioconda/bioconda-recipes

Update PacBio `zmwfilter` 1.0.0 rebuild

Rebuild zmwfilter with new dependencies.


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

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armintoepfer

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pull request commentbioconda/bioconda-recipes

Update PacBio `zmwfilter` 1.0.0 rebuild

@BiocondaBot please merge

armintoepfer

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pull request commentbioconda/bioconda-recipes

Update PacBio `zmwfilter` 1.0.0 rebuild

@BiocondaBot please fetch artifacts

armintoepfer

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push eventbioconda/bioconda-recipes

Armin Töpfer

commit sha fc0665d42a6569e602301c03b3393c87732c1fc2

Update PacBio `zmwfilter` 1.0.0 rebuild

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pull request commentbioconda/bioconda-recipes

Update PacBio `zmwfilter` 1.0.0 rebuild

@BiocondaBot please fetch artifacts

armintoepfer

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PR opened bioconda/bioconda-recipes

Reviewers
Update PacBio `zmwfilter` 1.0.0 rebuild

Rebuild zmwfilter with new dependencies.


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

<details> <summary>Please use the following BiocondaBot commands:</summary>

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

<table> <tr> <td><code>@BiocondaBot please update</code></td> <td>Merge the master branch into a PR.</td> </tr> <tr> <td><code>@BiocondaBot please add label</code></td> <td>Add the <code>please review & merge</code> label.</td> </tr> <tr> <td><code>@BiocondaBot please fetch artifacts</code></td> <td>Post links to CI-built packages/containers. <br />You can use this to test packages locally.</td> </tr> </table>

For members of the Bioconda project, the following command is also available:

<table> <tr> <td><code>@BiocondaBot please merge</code></td> <td>Upload built packages/containers and merge a PR. <br />Someone must approve a PR first! <br />This reduces CI build time by reusing built artifacts.</td> </tr> </table>

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

</details>

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create barnchbioconda/bioconda-recipes

branch : zmwfilter-1.0.0-1

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issue commentPacificBiosciences/pbbioconda

zmwfilter very slow

samtools index on an unaligned BAM always results in an empty BAI.

gevro

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issue commentPacificBiosciences/pbbioconda

zmwfilter very slow

I've rebuild with the latest dependencies. 20k ZMWs are now being filtered in 45s on my machine. Please let me know if that works and I'll upload to bioconda:

https://github.com/PacificBiosciences/zmwfilter/releases/tag/v1.0.0

gevro

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release PacificBiosciences/zmwfilter

v1.0.0

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issue closedPacificBiosciences/pbbioconda

pbindexdump - uses a lot of memory

pbindexdump uses a large amount of RAM. It crashes out of memory with 64 G RAM on a 2.7Gb pbi file. Seems like it should not take that much RAM to dump an index file.

It also sometimes crashes with "Bus error".

Also, it runs very slowly.

Perhaps this is the cause of zmwfilter being slow, if it is using the same underlying pbindexdump code

closed time in 5 days

gevro

issue commentPacificBiosciences/pbbioconda

pbindexdump - uses a lot of memory

pbindexdump is an internal tool and not used in production pipelines. We will have a look, but this is low priority. Will ping here if we find something

gevro

comment created time in 5 days

issue commentPacificBiosciences/pbbioconda

Lima terminate called without an active exception

Can you provide a minimal test example for me to reproduce? Instructions for uploading are on the main pbbioconda page. Thank you

zmz1988

comment created time in 5 days

issue commentPacificBiosciences/pbbioconda

pbmm2 - command line parser ERROR: unknown option 'alignment-threads' (and 'sort-threads' and 'secondary')

We'll update the docs soon, but in general, please have a look at pbmm2 --help

CharlesARoy

comment created time in 5 days

issue commentPacificBiosciences/pbbioconda

ccs-kinetics-bystrandify not getting installed with conda install pbbam

We will address it in the next update of pbbam. Thank you.

ddubocan

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issue closedPacificBiosciences/pbbioconda

PacBio sequence: synthesized strand or copied strand?

Hi, I have a very technical, but simple question: when the PacBio instrument records DNA sequences in the raw subreads file, are those the sequences of the DNA that is being synthesized, or the DNA that is being copied?

Additionally, after running pbccs with the --by-strand option, do the /fwd and /rev labels refer to the strand physically being synthesized by the polymerase, or is there a reverse complement step somewhere in the instrument code or in pbccs that transforms it to the sequence of the strand being copied?

Thanks.

closed time in 5 days

gevro

issue commentPacificBiosciences/pbbioconda

PacBio sequence: synthesized strand or copied strand?

We are reporting the base present in the molecule.

Regarding by-strand: https://github.com/PacificBiosciences/pbbioconda/issues/458

If that's not enough detail, please reach out to your field application specialist or tech support.

gevro

comment created time in 5 days

IssuesEvent

issue closedPacificBiosciences/pbbioconda

zmwfilter exponentially slower with more zmw holes

Hi, I've confirmed on four different machines, including with a high-speed SSD drive, that there is an issue with zmwfilter, in that it becomes exponentially slower once you start requesting tens of thousands of holes to retrieve. The issue is not noticeable with 1 or a few hundred holes. Only once you get to > 10,000 or so.

Also reported by another user: PacificBiosciences/zmwfilter#1

I don't think it is an issue with disk speed.

If the zmw holes are indexed, it should be much faster than a single pass through the subreads.BAM to retrieve them, but that does not seem to be the case.

Thanks.

closed time in 5 days

gevro

issue commentPacificBiosciences/pbbioconda

zmwfilter exponentially slower with more zmw holes

Duplicate of #461

gevro

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issue commentPacificBiosciences/pbbioconda

zmwfilter very slow

I'll file it internally. We'll come back when we have a solution.

gevro

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Armin Töpfer

commit sha d1ccf9f168434e1d803214430d2004448803f71f

Update README.md

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