I installed CONCOCT via bioconda today (23rd September 2021) and I ran into several errors when running the standard pipeline. I document these errors and list my solutions in case it might be helpful to anyone in future:
(1) Command:
concoct_coverage_table.py contigs_10K.bed ../Input/NCM*.bam > coverage_table.tsv
Error:
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Solution:
After some googling this seems to have to something to do with OpenSSL migration (see https://github.com/bioconda/bioconda-recipes/issues/13958 for discussion).
I fixed this issue by running:
conda install samtools
this updated the samtools version that was installed by default within the environment to a more recent version and fixed the issue.
(2) Command:
concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/
Error:
Traceback (most recent call last): File "/data/SBCS-HenryLab/Raphaella/Software/CondaEnv/CONCOCT/bin/concoct", line 6, in <module> import vbgmm ImportError: libmkl_rt.so: cannot open shared object file: No such file or directory
Solution:
conda install mkl
Hello,
I installed CONCOCT via bioconda today (23rd September 2021) and I ran into several errors when running the standard pipeline. I document these errors and list my solutions in case it might be helpful to anyone in future:
(1) Command:
concoct_coverage_table.py contigs_10K.bed ../Input/NCM*.bam > coverage_table.tsvError:samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directorySolution: After some googling this seems to have to something to do with OpenSSL migration (see https://github.com/bioconda/bioconda-recipes/issues/13958 for discussion). I fixed this issue by running:conda install samtoolsthis updated the samtools version that was installed by default within the environment to a more recent version and fixed the issue.(2) Command:
concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/Error:Traceback (most recent call last): File "/data/SBCS-HenryLab/Raphaella/Software/CondaEnv/CONCOCT/bin/concoct", line 6, in <module> import vbgmm ImportError: libmkl_rt.so: cannot open shared object file: No such file or directorySolution:conda install mkl