ZhengJinfang1220
commented
1 month ago Report
Hello, I am a new user of dbcan. While running the following command:
dbcan_utils CGC_abund -bt Bv_WXH_abund/Bv_WXH.depth.txt -i dbcan_result -a TPMI encountered the following error:Traceback (most recent call last): File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/bin/dbcan_utils", line 10, in <module> sys.exit(main()) File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/lib/python3.8/site-packages/dbcan/utils/utils.py", line 619, in main PUL_abundance(args) File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/lib/python3.8/site-packages/dbcan/utils/utils.py", line 493, in PUL_abundance PUL_abund.output_cgc_abund() File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/lib/python3.8/site-packages/dbcan/utils/utils.py", line 462, in output_cgc_abund cgc_standard_records.append(self.cgcid2cgc_standard[cgcid]) KeyError: 'TC'This error indicates that the self.cgcid2cgc_standard dictionary does not contain the key 'TC' when executing the output_cgc_abund function.
Additionally, while running:
dbcan_utils CGC_substrate_abund -bt Bv_WXH_abund/Bv_WXH.depth.txt -i dbcan_result -a TPMI encountered a similar error:Traceback (most recent call last): File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/bin/dbcan_utils", line 10, in <module> sys.exit(main()) File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/lib/python3.8/site-packages/dbcan/utils/utils.py", line 622, in main PUL_Substrate_abundance(args) File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/lib/python3.8/site-packages/dbcan/utils/utils.py", line 500, in PUL_Substrate_abundance PUL_abund.Cal_PUL_Substrate_Abundance() File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/dbcan/lib/python3.8/site-packages/dbcan/utils/utils.py", line 371, in Cal_PUL_Substrate_Abundance cgc_abunds = self.cgcid2seqabund[cgcid] ### list constis of sequence abundance KeyError: 'NODE_4_length_250273_cov_247.905346|CGC1'Can anyone please guide me on how to resolve these issues? Attached is the screenshot of my input file, the cgc_standard.out file. I noticed in a previous issue tracker that the input file for dbcan_utils CGC_abund is cgc_standard.out. However, I am unsure what the input should be for dbcan_utils CGC_substrate_abund.
Here is some additional information that might be helpful: I followed the protocol outlined in "Run from Raw Reads: Automated CAZyme and Glycan Substrate Annotation in Microbiomes: A Step-by-Step Protocol". However, I did not use all the software recommended in the tutorial. Instead, I utilized alternative software for some steps because I had pre-developed parts of the workflow. My workflow diagram is as follows:
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Hi, the error prompt is wired. I did not encounter this bug before. Could you share the data with me (zhengjinfang1220@gmail.com)?
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Hello, I am a new user of dbcan. While running the following command:
dbcan_utils CGC_abund -bt Bv_WXH_abund/Bv_WXH.depth.txt -i dbcan_result -a TPMI encountered the following error:This error indicates that the self.cgcid2cgc_standard dictionary does not contain the key 'TC' when executing the output_cgc_abund function.
Additionally, while running:
dbcan_utils CGC_substrate_abund -bt Bv_WXH_abund/Bv_WXH.depth.txt -i dbcan_result -a TPMI encountered a similar error:Can anyone please guide me on how to resolve these issues? Attached is the screenshot of my input file, the cgc_standard.out file. I noticed in a previous issue tracker that the input file for dbcan_utils CGC_abund is cgc_standard.out. However, I am unsure what the input should be for dbcan_utils CGC_substrate_abund.
Here is some additional information that might be helpful: I followed the protocol outlined in "Run from Raw Reads: Automated CAZyme and Glycan Substrate Annotation in Microbiomes: A Step-by-Step Protocol". However, I did not use all the software recommended in the tutorial. Instead, I utilized alternative software for some steps because I had pre-developed parts of the workflow. My workflow diagram is as follows:
Version information
No response