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Bowtie runs successfully without the --best option but fails when the --best option is included #142

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santataRU opened this issue Nov 27, 2024 · 0 comments

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@santataRU
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I am using Bowtie 1.3.1 (ARM64-compatible version installed via Conda) on a Mac Studio with an M1 chip. Bowtie runs successfully without the --best option but fails when the --best option is included. I would greatly appreciate any guidance on how to address this issue. Details are attached below:

(base) bieniaszlab@pauls-imac-2 nxsq % bowtie -f -v2 --best -m 1 -p 10 -S /Users/bieniaszlab/Documents/Xiao/CLIP/Index/hg38/bowtieindex/hg38_bowtie_index CLIP74BC6_col_trim CLIP74BC6_DDX42_hg38_m1.sam
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
zsh: trace trap bowtie -f -v2 --best -m 1 -p 10 -S CLIP74BC6_col_trim
(base) bieniaszlab@pauls-imac-2 nxsq %bowtie -f -v2 -m 1 -p 10 -S /Users/bieniaszlab/Documents/Xiao/CLIP/Index/hg38/bowtieindex/hg38_bowtie_index CLIP74BC6_col_trim CLIP74BC6_DDX42_hg38_m1.sam
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
reads processed: 1285326
reads with at least one alignment: 471583 (36.69%)
reads that failed to align: 813743 (63.31%)
reads with alignments suppressed due to -m: 346953 (26.99%)
Reported 124630 alignments
(base) bieniaszlab@pauls-imac-2 nxsq % bowtie --version
/opt/anaconda3/bin/bowtie-align-s version 1.3.1
64-bit
Built on VM-8b0b7afd3b
2024-07-17T07:14:12
Compiler: InstalledDir: /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1721200189988/_build_env/bin
Options: -O3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/anaconda3/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1721200189988/work=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=/opt/anaconda3=/usr/local/src/conda-prefix -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/anaconda3/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1721200189988/work=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=/opt/anaconda3=/usr/local/src/conda-prefix
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

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