It has been a nightmare to make CONCOCT running on a macOS computer. After a very painful installation, the following line will die on a SEGFAULT or a BUS error, depending if I put or not the thread option.
OPTION 1
/Users/tito_miniconda/programs/concoct/CONCOCT-1.1.0/bin/concoct -r 150 --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/ WARNING:root:CONCOCT is running in single threaded mode. Please, consider adjusting the --threads parameter. Up and running. Check /Volumes/Red_4TB/scratch_BK/CS_BACKUP/p31_anvio_metagenomes/OC26_EXPERIMENT/concoct_bins/concoct_output/log.txt for progress /Users/tito_miniconda/opt/miniconda3/envs/concoct_env/lib/python2.7/site-packages/concoct-1.1.0-py2.7-macosx-10.6-x86_64.egg/concoct/input.py:82: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. cov = p.read_table(cov_file, header=0, index_col=0) Bus error: 10
OPTION 2
/Users/tito_miniconda/programs/concoct/CONCOCT-1.1.0/bin/concoct -t 6 -r 150 --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/ Up and running. Check /Volumes/Red_4TB/scratch_BK/CS_BACKUP/p31_anvio_metagenomes/OC26_EXPERIMENT/concoct_bins/concoct_output/log.txt for progress /Users/tito_miniconda/opt/miniconda3/envs/concoct_env/lib/python2.7/site-packages/concoct-1.1.0-py2.7-macosx-10.6-x86_64.egg/concoct/input.py:82: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. cov = p.read_table(cov_file, header=0, index_col=0) Segmentation fault: 11
Any ideas on how to fix this? BTW, the log file does not show any clue about the details of the error. All very cryptic.
It has been a nightmare to make CONCOCT running on a macOS computer. After a very painful installation, the following line will die on a SEGFAULT or a BUS error, depending if I put or not the thread option.
OPTION 1
/Users/tito_miniconda/programs/concoct/CONCOCT-1.1.0/bin/concoct -r 150 --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/ WARNING:root:CONCOCT is running in single threaded mode. Please, consider adjusting the --threads parameter. Up and running. Check /Volumes/Red_4TB/scratch_BK/CS_BACKUP/p31_anvio_metagenomes/OC26_EXPERIMENT/concoct_bins/concoct_output/log.txt for progress /Users/tito_miniconda/opt/miniconda3/envs/concoct_env/lib/python2.7/site-packages/concoct-1.1.0-py2.7-macosx-10.6-x86_64.egg/concoct/input.py:82: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. cov = p.read_table(cov_file, header=0, index_col=0) Bus error: 10OPTION 2
/Users/tito_miniconda/programs/concoct/CONCOCT-1.1.0/bin/concoct -t 6 -r 150 --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/ Up and running. Check /Volumes/Red_4TB/scratch_BK/CS_BACKUP/p31_anvio_metagenomes/OC26_EXPERIMENT/concoct_bins/concoct_output/log.txt for progress /Users/tito_miniconda/opt/miniconda3/envs/concoct_env/lib/python2.7/site-packages/concoct-1.1.0-py2.7-macosx-10.6-x86_64.egg/concoct/input.py:82: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. cov = p.read_table(cov_file, header=0, index_col=0) Segmentation fault: 11Any ideas on how to fix this? BTW, the log file does not show any clue about the details of the error. All very cryptic.