google/deepconsensus issues and pull requests

#76 - issue with tensorflow

Issue - State: closed - Opened by corkdagga 7 months ago - 13 comments

#75 - Optimizing runtime on HPC

Issue - State: closed - Opened by sadams2013 10 months ago - 2 comments

#74 - About making ground truth.

Issue - State: closed - Opened by Crispy13 11 months ago - 2 comments

#73 - KeyError

Issue - State: closed - Opened by jferbe1 12 months ago - 5 comments

#72 - normal pass / fail rate?

Issue - State: closed - Opened by AlcaArctica about 1 year ago - 2 comments

#71 - OSError: error -3 while reading file

Issue - State: closed - Opened by daaaaande about 1 year ago - 8 comments

#70 - GPU installation using quick start guide fails

Issue - State: closed - Opened by ap1438 about 1 year ago - 5 comments

#69 - GPU installation failure with pip

Issue - State: closed - Opened by jsoghigian over 1 year ago - 3 comments

#68 - Separate subreads for mixed samples?

Issue - State: closed - Opened by icemduru over 1 year ago - 3 comments

#67 - bam or fastq issue

Issue - State: closed - Opened by HITzhongyu over 1 year ago - 2 comments

#66 - Change the wrong number of strand in the homepage image of pipeline_figure.

Pull Request - State: open - Opened by one-matrix over 1 year ago - 2 comments

#65 - the label without alignment

Issue - State: closed - Opened by one-matrix over 1 year ago - 5 comments

#64 - vRAM limit

Issue - State: closed - Opened by fergsc over 1 year ago - 1 comment

#63 - Cannot open/create ccs.bam file?

Issue - State: closed - Opened by scthree over 1 year ago - 6 comments

#62 - Public raw train dataset availability

Issue - State: closed - Opened by marcpaga almost 2 years ago - 2 comments

#61 - QV for each ccs reads

Issue - State: closed - Opened by Wenfei-Xian almost 2 years ago - 2 comments

#60 - install.sh for conda env

Pull Request - State: open - Opened by wyim-pgl almost 2 years ago - 1 comment

#59 - [Repeat] Running deepconsensus results in "free(): invalid pointer" error

Issue - State: closed - Opened by mjg0 almost 2 years ago - 17 comments

#58 - python 3.9

Issue - State: closed - Opened by hildebra almost 2 years ago - 2 comments

#57 - lower quality and less reads in deepconsensus 1.0 output compared to ccs

Issue - State: closed - Opened by daaaaande almost 2 years ago - 2 comments

#56 - Installation from source file problem

Issue - State: closed - Opened by ap1438 almost 2 years ago - 2 comments

#55 - Error detecting params.json using docker in debian (10) HPC

Issue - State: closed - Opened by ap1438 almost 2 years ago - 2 comments

#54 - Lower number of >Q30 average quality reads for v1.1 compared to v0.3

Issue - State: closed - Opened by mason-linscott almost 2 years ago - 10 comments

#53 - Use of samtools and awk to filter incorrect alignments.

Issue - State: closed - Opened by ap1438 almost 2 years ago - 2 comments

#52 - HPC resource managment not working with deepconsensus

Issue - State: closed - Opened by MmasterT almost 2 years ago

#51 - Update documentation to pip version 1.0.1

Pull Request - State: closed - Opened by pichuan almost 2 years ago

#50 - Fix a pip install issue reported in https://github.com/google/deepconsensus/issues/48

Pull Request - State: closed - Opened by pichuan almost 2 years ago

#49 - Missing majority of ZMWs after running lima to search for adapters

Issue - State: closed - Opened by rosspdu about 2 years ago - 4 comments

#48 - Running deepconsensus results in "free(): invalid pointer" error

Issue - State: closed - Opened by mjg0 about 2 years ago - 15 comments

#47 - Error: ModuleNotFoundError: No module named 'pandas._libs.interval'

Issue - State: closed - Opened by gevro about 2 years ago - 6 comments

#46 - Merge r1.0 into main.

Pull Request - State: closed - Opened by danielecook about 2 years ago - 1 comment

#45 - no subreads available

Issue - State: closed - Opened by michaelabrouk about 2 years ago - 2 comments

#44 - deepconsensus on metagenomic data

Issue - State: closed - Opened by ay-amityadav about 2 years ago - 2 comments

#43 - actc and kinetic data orientation

Issue - State: closed - Opened by gevro about 2 years ago - 2 comments

#42 - Missing about 30% of ZMWs in output

Issue - State: closed - Opened by gevro about 2 years ago - 2 comments

#41 - Strand of Fastq output

Issue - State: closed - Opened by gevro about 2 years ago - 2 comments

#40 - download params.json but Connection refused.

Issue - State: closed - Opened by ymwang233 about 2 years ago - 3 comments

#39 - Merging aligned fastq output with original ccs BAM

Issue - State: closed - Opened by gevro about 2 years ago - 2 comments

#38 - question about the permutation invariance in the MSA input to the DeepConsensus model

Issue - State: closed - Opened by rainwala about 2 years ago - 1 comment

#37 - Error: StopIteration

Issue - State: closed - Opened by gevro over 2 years ago - 5 comments

#36 - Error: ValueError: Shapes (2640, 280) and (560, 280) are incompatible

Issue - State: closed - Opened by gevro over 2 years ago - 15 comments

#35 - Error: model/params.json not found

Issue - State: closed - Opened by gevro over 2 years ago - 1 comment

#34 - Chunking with deepconsensus

Issue - State: closed - Opened by gevro over 2 years ago - 7 comments

#33 - R0.3.1

Pull Request - State: closed - Opened by danielecook over 2 years ago - 1 comment

#32 - Advice for dealing with barcode multiplexing

Issue - State: closed - Opened by peterdfields over 2 years ago - 3 comments

#31 - DeepConsensus 0.3 --min_quality has no default?

Issue - State: closed - Opened by MartinPippel over 2 years ago - 2 comments

#30 - Alignment loss function

Issue - State: closed - Opened by marcpaga over 2 years ago - 2 comments

#29 - Docker - tensorflow error

Issue - State: closed - Opened by AMMMachado over 2 years ago - 2 comments

#28 - CPU installation on HPC, no sudo, no docker/singularity

Issue - State: closed - Opened by abueg over 2 years ago - 7 comments

#27 - Training tutorial?

Issue - State: closed - Opened by jelber2 over 2 years ago - 11 comments

#26 - Update install_nvidia_docker.sh to version 1.4.

Pull Request - State: closed - Opened by MariaNattestad over 2 years ago

#25 - An tutorial for running deepconsensus

Issue - State: closed - Opened by shengxinzhuan over 2 years ago - 6 comments

#24 - can deepconsensus run on an arm machine？

Issue - State: closed - Opened by shengxinzhuan over 2 years ago - 6 comments

#23 - General performance question

Issue - State: closed - Opened by chenxf611 almost 3 years ago - 3 comments

#22 - DeepConsensus model is not accessed from China

Issue - State: closed - Opened by zhangrengang almost 3 years ago - 2 comments

#21 - params.json and checkpoint sample files

Issue - State: closed - Opened by peterdfields almost 3 years ago - 1 comment

#20 - BrokenPipeError: [Errno 32] Broken pipe

Issue - State: closed - Opened by AhmedArslan almost 3 years ago - 2 comments

#19 - Error (ccs software) - No space left on device (tmp file).

Issue - State: closed - Opened by AMMMachado almost 3 years ago - 12 comments

#18 - general performance question and --cpu flag is not working

Issue - State: closed - Opened by MartinPippel almost 3 years ago - 4 comments

#17 - deepconsensus-0.2.0 uses a lot of system RAM, so maybe best to split jobs into pieces, example provided

Issue - State: closed - Opened by jelber2 almost 3 years ago - 4 comments

#16 - deepconsensus-0.2.0 complains that subreads_to_ccs.bam is not indexed

Issue - State: closed - Opened by jelber2 almost 3 years ago - 2 comments

#15 - Docker or Singularity

Issue - State: closed - Opened by AMMMachado almost 3 years ago - 5 comments

#14 - How to improve run time?

Issue - State: closed - Opened by MartinPippel almost 3 years ago - 1 comment

#13 - deepconsensus.scripts.run_deepconsensus errors

Issue - State: closed - Opened by zhoudreames about 3 years ago - 2 comments

#12 - Support FOFN original subread input, document CLI

Issue - State: closed - Opened by maximilianpress about 3 years ago - 2 comments

GitHub / google/deepconsensus issues and pull requests