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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
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celescope vdj mapping_vdj CalledProcessError error #248

Open liujiayu1997 opened 1 year ago

liujiayu1997 commented 1 year ago

Describe the bug When I run the command : celescope vdj mapping_vdj --outdir ./Zhoujianxin_GC/04.mapping_vdj --sample Zhoujianxin_GC --thread 8 --ref_path "/mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR" --type TCR --species human --fasta ./mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/Zhoujianxin_GC/03.consensus/Zhoujianxin_GC_consensus.fasta

I get the error like this: Args: Namespace(subparser_assay='vdj', ref_path='/mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR', type='TCR', species='human', split_fasta=False, fasta='./mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/Zhoujianxin_GC/03.consensus/Zhoujianxin_GC_consensus.fasta', outdir='./Zhoujianxin_GC/04.mapping_vdj', sample='Zhoujianxin_GC', thread='1', debug=False, func=<function mapping_vdj at 0x7f0521fdfe20>) 2023-07-09 13:39:50,596 - celescope.vdj.mapping_vdj.igblast - INFO - start... 2023-07-09 13:39:50,596 - celescope.vdj.mapping_vdj.igblast - INFO - igblastn -query ./mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/Zhoujianxin_GC/03.consensus/Zhoujianxin_GC_consensus.fasta -organism human -ig_seqtype TCR -auxiliary_data optional_file/human_gl.aux -num_threads 1 -germline_db_V /mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR/TRV.fa -germline_db_D /mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR/TRD.fa -germline_db_J /mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR/TRJ.fa -domain_system imgt -show_translation -outfmt 19 -out ./Zhoujianxin_GC/04.mapping_vdj/Zhoujianxin_GC_airr.tsv BLAST query/options error: Germline annotation database human/human_TR_V could not be found in [internal_data] directory Please refer to the BLAST+ user manual. 2023-07-09 13:39:51,891 - celescope.tools.step._clean_up - INFO - start... 2023-07-09 13:39:51,893 - celescope.tools.step._render_html - INFO - start... 2023-07-09 13:39:52,295 - celescope.tools.step._render_html - INFO - done. time used: 0:00:00.402076 2023-07-09 13:39:52,295 - celescope.tools.step._clean_up - INFO - done. time used: 0:00:00.404104 Traceback (most recent call last): File "/home/xiaying/anaconda3/envs/Celescope/bin/celescope", line 8, in sys.exit(main()) ^^^^^^ File "/home/xiaying/anaconda3/envs/Celescope/lib/python3.11/site-packages/celescope/celescope.py", line 43, in main args.func(args) File "/home/xiaying/anaconda3/envs/Celescope/lib/python3.11/site-packages/celescope/vdj/mapping_vdj.py", line 220, in mapping_vdj runner.run() File "/home/xiaying/anaconda3/envs/Celescope/lib/python3.11/site-packages/celescope/vdj/mapping_vdj.py", line 56, in run self.igblast(fasta=self.args.fasta, airr_out=self.airr_out[0]) File "/home/xiaying/anaconda3/envs/Celescope/lib/python3.11/site-packages/celescope/tools/utils.py", line 46, in wrapper result = func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/xiaying/anaconda3/envs/Celescope/lib/python3.11/site-packages/celescope/vdj/mapping_vdj.py", line 105, in igblast subprocess.check_call(cmd, shell=True) File "/home/xiaying/anaconda3/envs/Celescope/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'igblastn -query ./mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/Zhoujianxin_GC/03.consensus/Zhoujianxin_GC_consensus.fasta -organism human -ig_seqtype TCR -auxiliary_data optional_file/human_gl.aux -num_threads 1 -germline_db_V /mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR/TRV.fa -germline_db_D /mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR/TRD.fa -germline_db_J /mnt/b95b4929-e82a-40e3-aa94-c772e90d8aeb/cellranger/xingeyuan/TCR/vdj/TR/TRJ.fa -domain_system imgt -show_translation -outfmt 19 -out ./Zhoujianxin_GC/04.mapping_vdj/Zhoujianxin_GC_airr.tsv ' returned non-zero exit status 1.

I don't know how to solve it, my igblastn version is 1.18.0 or 1.21.0, but neither of this version work.

Chenjunjie1996 commented 1 year ago

Did you build reference successfully before running? https://github.com/singleron-RD/CeleScope/blob/master/doc/assay/multi_vdj.md