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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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AssertionError: Species not found in resources #59

Closed zhouxinseeu closed 3 years ago

zhouxinseeu commented 3 years ago

Hi! When I test bracer, the error occured:

$ bracer test -p 8 -c bracer.conf 
Traceback (most recent call last):
  File "/SGRNJ/Public/Software/conda_env/Bracer/bin/bracer", line 33, in <module>
    sys.exit(load_entry_point('bracer==0.1', 'console_scripts', 'bracer')())
  File "/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/tasks.py", line 2008, in run
    trimmed_fastq2=self.trimmed_fastq2).run()
  File "/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/tasks.py", line 298, in __init__
    root=resource_dir)
  File "/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/bracer-0.1-py3.7.egg/bracerlib/tasks.py", line 184, in get_species_root
    assert os.path.isdir(resources_root), "Species not found in resources"
AssertionError: Species not found in resources

and my conf file content:

$ cat bracer.conf 
#Configuration file for BraCeR#

[tool_locations]
#paths to tools used by BraCeR for alignment, quantitation, etc
bowtie2_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/bowtie2
igblastn_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/igblastn
blastn_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/blastn
kallisto_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/kallisto
trinity_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/Trinity
dot_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/dot
neato_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/neato
changeo_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/
rscript_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/Rscript
dnapars_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/phylip
trim_galore_path = /SGRNJ/Public/Software/conda_env/Bracer/bin/trim_galore
cutadapt_path = /SGRNJ01/Public/Software/anaconda3/bin/cutadapt

[trinity_options]
#line below specifies maximum memory for Trinity Jellyfish component. Set it appropriately for your environment.
max_jellyfish_memory = 10G

[kallisto_transcriptomes]
Hsap = /Personal/zhouxin/software/bracer/Transcriptome_reference/Hsap/transcripts.fasta
Mmus = /Personal/zhouxin/software/bracer/Transcriptome_reference/Mmus/transcripts.fasta

[bracer_location]
#Path to where BraCeR was originally installed
bracer_path = /Personal/zhouxin/software/bracer/bracer

I have tried specified the path of bracer and bracer.conf, but it also failed