ImportError:undefined symbol: BrotliSharedDictionaryDestroyInstance

[jiangjasson]

你好，我在运行run步骤遇到了问题 这是我的运行代码 (dnbc4tools) dell@dell-Precision-7920-Tower:~/Documents/jiangss/script/dnbc4toolsscript$ cat 2.dnbc4tools_rna_run.sh

dnbc4tools rna run --cDNAfastq1 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/cDNA/H1Ascl1clone4_S1_L001_1.fq.gz --cDNAfastq2 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/cDNA/H1Ascl1clone4_S1_L001_2.fq.gz --oligofastq1 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/oligo/H1Ascl1clone4_S1_L001_1.fq.gz --oligofastq2 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/oligo/H1Ascl1clone4_S1_L001_2.fq.gz --genomeDir /home/dell/Documents/jiangss/reference/dnbc4-genome/GRCh38-gencodev46-mCherry708 --name H1ASCL1PNEC --threads 90 1>dncbrnarun.log 2>&1

我看了下报错的内容，是ImportError: /home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/pyarrow/../../.././libbrotlidec.so.1: undefined symbol: BrotliSharedDictionaryDestroyInstance

以下是具体的报错内容： Chemistry(darkreaction) determined in oligoR1 : darkreaction Chemistry(darkreaction) determined in oligoR2 : darkreaction Chemistry(darkreaction) determined in cDNAR1 : darkreaction

2024-06-26 09:34:31 Conduct quality control for cDNA library barcoding, perform alignment.

2024-06-26 09:34:31 Perform quality control for oligo library barcodes.

2024-06-26 10:32:24 Annotate gene regions for the aligned BAM. Traceback (most recent call last): File "/home/dell/anaconda3/envs/dnbc4tools/bin/dnbc4tools", line 8, in sys.exit(main()) File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/dnbc4tools.py", line 110, in main args.func(args) File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/data.py", line 169, in data Data(args).run() File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/data.py", line 157, in run oligo_combine_pl(f"{__root_dir}/config/cellbarcode/oligo_type.json", File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/tools/utils.py", line 183, in wrapper result = func(*args, **kwargs) File "oligo_filter.py", line 355, in dnbc4tools.rna.src.oligo_filter.oligo_combine_pl File "oligo_filter.py", line 280, in dnbc4tools.rna.src.oligo_filter.OligoCombiner.polars_CBUB File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/polars/dataframe/frame.py", line 2238, in to_pandas record_batches = self._df.to_pandas() File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/pyarrow/init__.py", line 65, in import pyarrow.lib as _lib ImportError: /home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/pyarrow/../../.././libbrotlidec.so.1: undefined symbol: BrotliSharedDictionaryDestroyInstance Traceback (most recent call last): File "/home/dell/anaconda3/envs/dnbc4tools/bin/dnbc4tools", line 8, in sys.exit(main()) File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/dnbc4tools.py", line 110, in main args.func(args) File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/run.py", line 144, in run Runpipe(args).runpipe() File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/run.py", line 131, in runpipe start_print_cmd(pipecmd,os.path.join(self.outdir,self.name)) File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/tools/utils.py", line 138, in start_print_cmd subprocess.check_call(arg, shell=True) File "/home/dell/anaconda3/envs/dnbc4tools/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/dell/anaconda3/envs/dnbc4tools/bin/dnbc4tools rna data --cDNAfastq1 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/cDNA/H1Ascl1clone4_S1_L001_1.fq.gz --cDNAfastq2 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/cDNA/H1Ascl1clone4_S1_L001_2.fq.gz --oligofastq1 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/oligo/H1Ascl1clone4_S1_L001_1.fq.gz --oligofastq2 /mnt/disk1/dataset/H1-ASCL1-Clone4-PNEC/rawdata/oligo/H1Ascl1clone4_S1_L001_2.fq.gz --threads 90 --name H1ASCL1PNEC --chemistry auto --darkreaction auto --outdir /home/dell/Documents/jiangss/project/H1-Ascl1-mCherry-clone4 --genomeDir /home/dell/Documents/jiangss/reference/dnbc4-genome/GRCh38-gencodev46-mCherry708 --gtf /home/dell/Documents/jiangss/reference/GencodeRef/DNBC4_format/gencode.v46.primary_assembly.annotation.filter.mCherry.gtf --chrMT chrM' returned non-zero exit status 1.

我是从Gencode下载fasta和gtf文件，往里面加了一个荧光基因，然后生成了参考基因组，这一步没有报错，成功生成了，在run这一步报错结束时，生成的01.data文件如下：

log目录的文件: 20240626.txt bt_log.txt

这是我的conda环境中的包： conda_list.txt

请问要如何解决呢?

[jiangjasson]

我查看了下dnbc4tools环境中的brotli的版本，显示没有，在base环境中有

[lishuangshuang0616]

好像是你的base与环境里面的这个so冲突了。能否删除这个环境，重新使用过这个方法安装而不是yaml呢

[jiangjasson]

好像是你的base与环境里面的这个so冲突了。能否删除这个环境，重新使用过这个方法安装而不是yaml呢

非常感谢，删除环境后，不使用yaml重装，就没报错了