Ecosyste.ms: Issues

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GitHub / hzi-bifo/RiboDetector issues and pull requests

#55 - An error occurred while executing the ribodetector_cpu command.

Issue - State: open - Opened by kinako0130 2 months ago - 5 comments

#54 - error after 14 hours of processing

Issue - State: closed - Opened by tulikasriv26 5 months ago - 3 comments

#53 - unexpected large proportion of rRNA reads detected by RiboDetector

Issue - State: closed - Opened by Ivy-ops 6 months ago - 13 comments

#52 - Log file/progress formatting for better readability

Issue - State: open - Opened by mckellardw 9 months ago - 2 comments

#51 - RiboDetector for barcoded libraries

Issue - State: closed - Opened by mckellardw 10 months ago - 2 comments
Labels: enhancement

#50 - Mouse data compatibility

Issue - State: closed - Opened by mmiots9 11 months ago - 2 comments

#49 - No classification at all for some data and classification for some

Issue - State: closed - Opened by EorgeKit 11 months ago - 6 comments

#48 - Read Length question

Issue - State: closed - Opened by singhbhavya 12 months ago - 1 comment

#46 - Address already in use

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

#45 - Classification of the rRNA removed seqeunces

Issue - State: closed - Opened by LeoVincenzi about 1 year ago - 3 comments

#44 - Tuple range error

Issue - State: closed - Opened by mwylerCH about 1 year ago - 3 comments

#43 - Can we apply this tool for custom reference sequences?

Issue - State: closed - Opened by ssun1116 about 1 year ago - 2 comments

#41 - Can we use Ribodetector for rRNA quantification in scRNASeq?

Issue - State: closed - Opened by Rohit-Satyam over 1 year ago - 1 comment
Labels: enhancement

#40 - RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)

Issue - State: closed - Opened by caldodge over 1 year ago - 9 comments
Labels: pytorch

#38 - Retrive the filtered out sequences

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

#37 - RiboDetector is identifying reads generated from ChrX and ChrY as rRNA reads

Issue - State: closed - Opened by rajanbit over 1 year ago - 4 comments

#35 - Change the log info, from detect_cpu to ribodetector_cpu

Issue - State: closed - Opened by dawnmy over 1 year ago

#34 - RiboDetector is not working on GPU mode

Issue - State: closed - Opened by Nirmal2310 over 1 year ago - 4 comments

#33 - Ability to produce a log file that can be easily processed by MultiQC

Issue - State: closed - Opened by Rohit-Satyam almost 2 years ago - 18 comments
Labels: bug, documentation, enhancement

#31 - ribodetector_cpu hangs with SLURM

Issue - State: closed - Opened by gianfilippo almost 2 years ago - 4 comments

#30 - Recommendations on running RiboDetector twice on the fastq files?

Issue - State: closed - Opened by resol341 almost 2 years ago - 2 comments

#28 - Which organism?

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

#27 - Chunk size question

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

#26 - gzip is very slow

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

#25 - Question

Issue - State: closed - Opened by deoliveira86 over 2 years ago - 2 comments

#24 - Using RiboDetector on assembled contigs?

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

#23 - question regarding confidence of -e norrna option

Issue - State: closed - Opened by caity-s over 2 years ago - 4 comments

#22 - docker image for 0.2.6

Issue - State: closed - Opened by NicoleGruenheit over 2 years ago - 3 comments
Labels: docker

#21 - False postivies when using on metagenomic data?

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

#20 - About read length

Issue - State: closed - Opened by gouwei1 over 2 years ago - 2 comments

#19 - Is it possible using Ribodector on metagenomic reads

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

#18 - CPU mode hangs with macOS

Issue - State: closed - Opened by omicz over 2 years ago - 6 comments
Labels: onnxruntime, MacOS

#17 - cpu vs. gpu performance

Issue - State: closed - Opened by ARW-UBT over 2 years ago - 4 comments

#16 - read length should be not smaller than 50, but ribo-seq reads are ~30 bp

Issue - State: closed - Opened by huguanjing over 2 years ago - 4 comments
Labels: enhancement, question

#15 - Installation error in conda environemnt

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

#14 - Add model eval?

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

#13 - In CPU mode, smaller chunk_size does not reduce the memory use.

Issue - State: closed - Opened by dawnmy almost 3 years ago - 3 comments
Labels: enhancement

#12 - Memory Calculation Doubts

Issue - State: closed - Opened by magcurly almost 3 years ago - 7 comments

#11 - no rRNA sequences were detected in an almost complete genome

Issue - State: closed - Opened by ThomasYJK555 almost 3 years ago - 2 comments

#10 - Add chunk size support for loading the sequences to reduce memory use for large files

Issue - State: closed - Opened by dawnmy almost 3 years ago - 2 comments
Labels: enhancement

#9 - Memory issues with RiboDetector

Issue - State: closed - Opened by akrinos almost 3 years ago - 23 comments
Labels: bug, enhancement, onnxruntime, SLURM

#8 - GPU with higher CUDA version can not be used within old pytorch

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

#7 - Lost reads?

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

#6 - Process hangs in CPU detection step

Issue - State: closed - Opened by sjaenick almost 3 years ago - 23 comments
Labels: bug, question, onnxruntime, SLURM

#5 - Optimize for CPU which supports AVX2 instruction

Issue - State: open - Opened by dawnmy about 3 years ago
Labels: enhancement

#4 - Training for next main release

Issue - State: closed - Opened by dawnmy about 3 years ago

#3 - Add tests

Issue - State: open - Opened by dawnmy over 3 years ago
Labels: documentation

#2 - Train for long reads e.g. nanopore, pacbio

Issue - State: open - Opened by dawnmy almost 4 years ago - 6 comments
Labels: enhancement

#1 - Add previous high divergent rRNA sequences in training

Issue - State: open - Opened by dawnmy almost 4 years ago
Labels: enhancement