Closed EllistonV closed 1 year ago
Hello,
I am having troubles while trying to run the following command:
medaka_consensus -i sample.fastq -d assembly.fasta -o clean -m r941_min_fast_g303 I get the following result:
medaka_consensus -i sample.fastq -d assembly.fasta -o clean -m r941_min_fast_g303
Checking program versions Program Version Required Pass minimap2 2.11 2.11 True samtools 1.3.1 1.3.1 True Aligning basecalls to draft Constructing minimap index. [M::mm_idx_gen::0.083*1.01] collected minimizers [M::mm_idx_gen::0.098*1.29] sorted minimizers [M::main::0.129*1.22] loaded/built the index for 1 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.135*1.21] distinct minimizers: 623917 (98.43% are singletons); average occurrences: 1.032; average spacing: 5.347 [M::main] Version: 2.11-r797 [M::main] CMD: minimap2 -I 16G -x map-ont --MD -d /home/ExtraDrive/PhdStudent4/medaka/assembly.fasta.mmi /home/ExtraDrive/PhdStudent4/medaka/assembly.fasta [M::main] Real time: 0.139 sec; CPU: 0.167 sec [samfaipath] build FASTA index... [M::main::0.030*1.03] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.038*1.02] mid_occ = 12 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.044*1.02] distinct minimizers: 623917 (98.43% are singletons); average occurrences: 1.032; average spacing: 5.347 [M::worker_pipeline::131.994*0.65] mapped 79732 sequences [M::main] Version: 2.11-r797 [M::main] CMD: minimap2 -x map-ont --MD -t 1 -a /home/ExtraDrive/PhdStudent4/medaka/assembly.fasta.mmi /home/ExtraDrive/PhdStudent4/medaka/sample.fastq [M::main] Real time: 132.001 sec; CPU: 85.680 sec [bam_sort_core] merging from 2 files... Running medaka consensus Traceback (most recent call last): File "/home/phdstudent4/.conda/envs/maria2/bin/medaka", line 7, in <module> from medaka.medaka import main File "/home/phdstudent4/.conda/envs/maria2/lib/python3.6/site-packages/medaka/medaka.py", line 10, in <module> from medaka.inference import train, predict File "/home/phdstudent4/.conda/envs/maria2/lib/python3.6/site-packages/medaka/inference.py", line 22, in <module> from medaka.features import SampleGenerator File "/home/phdstudent4/.conda/envs/maria2/lib/python3.6/site-packages/medaka/features.py", line 23, in <module> import libmedaka ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
I do not know what it means by ImportError. Am I missing a package or something? In advance, thanks!
ImportError
Hi @EllistonV,
Please open a new issue and fill out the template, this will help us to assist you.
Hello,
I am having troubles while trying to run the following command:
medaka_consensus -i sample.fastq -d assembly.fasta -o clean -m r941_min_fast_g303
I get the following result:I do not know what it means by
ImportError
. Am I missing a package or something? In advance, thanks!