Jianshu_Zhao

Hello Miguel, Is there a reason that aai.rb support gz files while ani.rb does not? This is very useful in many cases, especially when we have large number of genomes...

A binary

2

Hello phylodm team, it would be nice to have a binary to call from other languages like R, where wrapping rust libraries is not so easy. Thanks, Jianshu

parallel reading 10G fasta/fastq file

5

Dear seq_io team, I have many 10G fasta/fastq files (10,000) and I want to read each file in parallel (the order of each record in the file does not matter)...

conda install error

6

Hello Team, It seems under conda environment, it cannot be installed: installing *source* package ‘polyclip’ ... ** using staged installation compiling under C++11 checking whether the C++ compiler works... no...

hi Joel, Please see the following error: [2021-02-01 03:51:56 AM] INFO: Command: /vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/bin/enrichm enrichment --output ../representatives_functional_analysis_enrichM_ko_diamond_enrichment --annotate_output ../representatives_functional_analysis_enrichM_ko_diamond/ --metadata genome_name.txt --abundance pico_131_132_abundance.txt --processes 64 --ko [2021-02-01 03:51:56 AM] INFO: Running...

0.5.1 run error

2

enrichm annotate --output ./dereplicated_genomes_enrichm_annotate --genome_directory ./dereplicated_genomes --ko --pfam --tigrfam --hypothetical --cazy --threads 2 --parallel 10 error: Traceback (most recent call last): File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/bin/enrichm", line 4, in __import__('pkg_resources').run_script('enrichm==0.5.1', 'enrichm') File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/pkg_resources/__init__.py",...

Hi Zekun, Just curious whether it is possible to also accelerate bindash via SIMD: https://github.com/zhaoxiaofei/bindash The bit xor operation now is already instruction-level optimized when compare two sketches. But not...

support for aarch64 (Neon)?

2

Dear RabbitMash team, Thanks for making Mash so fast! I am wondering whether it also supports aarch64 like cpu instructions, for example, macOS M1/M2 series and Linux aarch64 (e.g., Huawei...

update to ahash 0.8.7 or after to use new stdsimd feature portable_simd

1

Dear Hashbrown team, It seems when rely ahash for high performance, ahash 0.8.6 is not compatible with newest nightly rust 1.78 which is now portable_simd for the old stdsimd features....

Hello @alecmocatta, Since the nightly Rust v1.78, feature stdsimd does not exists any more: error[E0557]: feature has been removed --> /Users/jianshuzhao/.cargo/registry/src/index.crates.io-6f17d22bba15001f/packed_simd-0.3.9/src/lib.rs:218:5 | 218 | platform_intrinsics, | ^^^^^^^^^^^^^^^^^^^ feature has been...