I have installed bracer in my local machine and I am trying the test
python bracer test -p 2 -c bracer.conf run
to see if everything worked fine.
After mapping and trinity assembly there is the step of blasting the assembled sequences. While running igblast, Bracer is running MakeDb.py, but it cannot recognize the options --regions --scores that I believe are included in bracer while running MakeDb.py. You can see the error below MakeDb.py: error: unrecognized arguments: --regions --scores:
usage: MakeDb.py [--version] [-h] ...
MakeDb.py: error: unrecognized arguments: --regions --scores
Traceback (most recent call last):
File "bracer", line 21, in <module>
launch()
File "/site/ne/home/i0439277/bracer/bracer-master/bracerlib/launcher.py", line 43, in launch
Task().run()
File "/site/ne/home/i0439277/bracer/bracer-master/bracerlib/tasks.py", line 2008, in run
trimmed_fastq2=self.trimmed_fastq2).run()
File "/site/ne/home/i0439277/bracer/bracer-master/bracerlib/tasks.py", line 374, in run
cell = self.ig_blast() # Run IgBlast
File "/site/ne/home/i0439277/bracer/bracer-master/bracerlib/tasks.py", line 547, in ig_blast
self.create_changeo_db()
File "/site/ne/home/i0439277/bracer/bracer-master/bracerlib/tasks.py", line 581, in create_changeo_db
ungapped_seq_location, self.cell_name)
File "/site/ne/home/i0439277/bracer/bracer-master/bracerlib/bracer_func.py", line 2234, in run_MakeDb_for_cell
subprocess.check_call(command)
File "/site/ne/home/i0439277/anaconda3/envs/bracer_env/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['MakeDb.py', 'igblast', '-i', '/site/ne/home/i0439277/bracer/bracer-master/test_data/results/cell1/IgBLAST_output/cell1_BCR_K.fmt7', '-s', '/site/ne/home/i0439277/bracer/bracer-master/test_data/results/cell1/Trinity_output/cell1_BCR_K.Trinity.fasta', '-r', '/site/ne/home/i0439277/bracer/bracer-master/resources/Hsap/imgt_gapped_resources/raw_seqs/BCR_K_V.fa', '/site/ne/home/i0439277/bracer/bracer-master/resources/Hsap/raw_seqs/BCR_H_D.fa', '/site/ne/home/i0439277/bracer/bracer-master/resources/Hsap/raw_seqs/BCR_K_J.fa', '--regions', '--scores']' returned non-zero exit status 2.
If I run the same command removing --regions --scores it works:
Hello,
I have installed bracer in my local machine and I am trying the test
python bracer test -p 2 -c bracer.conf run
to see if everything worked fine.
After mapping and trinity assembly there is the step of blasting the assembled sequences. While running igblast, Bracer is running MakeDb.py, but it cannot recognize the options --regions --scores that I believe are included in bracer while running MakeDb.py. You can see the error below MakeDb.py: error: unrecognized arguments: --regions --scores:
If I run the same command removing
--regions --scores
it works:Has anyone encountered the same issue? How can avoid it? Thank you for any feedback. I am open to modify that part in the software.