Open jianshu93 opened 3 years ago
hi Joel,
Please see the following error:
[2021-02-01 03:51:56 AM] INFO: Command: /vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/bin/enrichm enrichment --output ../representatives_functional_analysis_enrichM_ko_diamond_enrichment --annotate_output ../representatives_functional_analysis_enrichM_ko_diamond/ --metadata genome_name.txt --abundance pico_131_132_abundance.txt --processes 64 --ko [2021-02-01 03:51:56 AM] INFO: Running the enrichment pipeline [2021-02-01 03:51:56 AM] INFO: Parsing annotate output: ../representatives_functional_analysis_enrichM_ko_diamond/ [2021-02-01 03:51:59 AM] INFO: Parsing metadata: genome_name.txt [2021-02-01 03:51:59 AM] INFO: Running abundances pipeline [2021-02-01 03:51:59 AM] INFO: Parsing sample abundance [2021-02-01 03:51:59 AM] INFO: Parsing sample metadata Traceback (most recent call last): File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/bin/enrichm", line 4, in import('pkg_resources').run_script('enrichm==0.5.1', 'enrichm') File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/pkg_resources/init.py", line 665, in run_script self.require(requires)[0].run_script(script_name, ns) File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/pkg_resources/init.py", line 1463, in run_script exec(code, namespace, namespace) File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/EGG-INFO/scripts/enrichm", line 342, in main() File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/EGG-INFO/scripts/enrichm", line 340, in main run.run_enrichm(args, sys.argv) File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/enrichm/run.py", line 399, in run_enrichm args.output) File "/vd03/home/jianshu/anaconda33/install_withtear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/enrichm/enrichment.py", line 379, in do , _, ab_attribute_dict = Parser.parse_metadata_matrix(abundance_metadata_path) File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/enrichm/parser.py", line 114, in parse_metadata_matrix with open(matrix_path) as matrix_file_io: TypeError: expected str, bytes or os.PathLike object, not NoneType
genome_name.txt pico_131_132_abundance.txt
hi Joel,
Please see the following error:
[2021-02-01 03:51:56 AM] INFO: Command: /vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/bin/enrichm enrichment --output ../representatives_functional_analysis_enrichM_ko_diamond_enrichment --annotate_output ../representatives_functional_analysis_enrichM_ko_diamond/ --metadata genome_name.txt --abundance pico_131_132_abundance.txt --processes 64 --ko [2021-02-01 03:51:56 AM] INFO: Running the enrichment pipeline [2021-02-01 03:51:56 AM] INFO: Parsing annotate output: ../representatives_functional_analysis_enrichM_ko_diamond/ [2021-02-01 03:51:59 AM] INFO: Parsing metadata: genome_name.txt [2021-02-01 03:51:59 AM] INFO: Running abundances pipeline [2021-02-01 03:51:59 AM] INFO: Parsing sample abundance [2021-02-01 03:51:59 AM] INFO: Parsing sample metadata Traceback (most recent call last): File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/bin/enrichm", line 4, in
import('pkg_resources').run_script('enrichm==0.5.1', 'enrichm')
File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/pkg_resources/init.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/pkg_resources/init.py", line 1463, in run_script
exec(code, namespace, namespace)
File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/EGG-INFO/scripts/enrichm", line 342, in
main()
File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/EGG-INFO/scripts/enrichm", line 340, in main
run.run_enrichm(args, sys.argv)
File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/enrichm/run.py", line 399, in run_enrichm
args.output)
File "/vd03/home/jianshu/anaconda33/install_withtear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/enrichm/enrichment.py", line 379, in do
, _, ab_attribute_dict = Parser.parse_metadata_matrix(abundance_metadata_path)
File "/vd03/home/jianshu/anaconda33/install_with_tear/envs/enrichm/lib/python3.7/site-packages/enrichm-0.5.1-py3.7.egg/enrichm/parser.py", line 114, in parse_metadata_matrix
with open(matrix_path) as matrix_file_io:
TypeError: expected str, bytes or os.PathLike object, not NoneType
genome_name.txt pico_131_132_abundance.txt