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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Velvet indexError: list index out of range #186

Closed Ofsm closed 4 years ago

Ofsm commented 4 years ago

Hello again, I try to assembly some data with velvet and I get this message after one sp was successfully assembled:

(phyluce) name@oscarpc:~/uce-tuto$ phyluce_assembly_assemblo_velvet \

--config assembly.conf \
--output velvet-assemblies \
--kmer 35 \
--subfolder split-adapter-quality-trimmed \
--cores 2 \
--clean \
--log-path log_velvet

2020-02-22 14:30:42,120 - phyluce_assembly_assemblo_velvet - INFO - =========== Starting phyluce_assembly_assemblo_velvet =========== 2020-02-22 14:30:42,121 - phyluce_assembly_assemblo_velvet - INFO - Version: 1.6.8 2020-02-22 14:30:42,121 - phyluce_assembly_assemblo_velvet - INFO - Argument --clean: True 2020-02-22 14:30:42,122 - phyluce_assembly_assemblo_velvet - INFO - Argument --config: /PATH/uce-tuto/assembly.conf 2020-02-22 14:30:42,122 - phyluce_assembly_assemblo_velvet - INFO - Argument --cores: 2 2020-02-22 14:30:42,122 - phyluce_assembly_assemblo_velvet - INFO - Argument --dir: None 2020-02-22 14:30:42,122 - phyluce_assembly_assemblo_velvet - INFO - Argument --kmer: 35 2020-02-22 14:30:42,122 - phyluce_assembly_assemblo_velvet - INFO - Argument --log_path: /PATH/uce-tuto/log_velvet 2020-02-22 14:30:42,122 - phyluce_assembly_assemblo_velvet - INFO - Argument --output: /PATH/uce-tuto/velvet-assemblies 2020-02-22 14:30:42,123 - phyluce_assembly_assemblo_velvet - INFO - Argument --subfolder: split-adapter-quality-trimmed 2020-02-22 14:30:42,123 - phyluce_assembly_assemblo_velvet - INFO - Argument --verbosity: INFO 2020-02-22 14:30:42,123 - phyluce_assembly_assemblo_velvet - INFO - Getting input filenames and creating output directories 2020-02-22 14:30:42,126 - phyluce_assembly_assemblo_velvet - INFO - --------------- Processing Hemicaecilius_mockfordi -------------- 2020-02-22 14:30:42,126 - phyluce_assembly_assemblo_velvet - INFO - Finding fastq/fasta files 2020-02-22 14:30:42,129 - phyluce_assembly_assemblo_velvet - INFO - File type is fastq 2020-02-22 14:30:42,130 - phyluce_assembly_assemblo_velvet - INFO - Running velveth against data 2020-02-22 14:36:32,121 - phyluce_assembly_assemblo_velvet - INFO - Running velvetg against data 2020-02-22 14:44:33,669 - phyluce_assembly_assemblo_velvet - INFO - Symlinking assembled contigs into /PATH/uce-tuto/velvet-assemblies/contigs 2020-02-22 14:44:33,670 - phyluce_assembly_assemblo_velvet - INFO - ---------------- Processing Lachesilla_texcocana ---------------- 2020-02-22 14:44:33,670 - phyluce_assembly_assemblo_velvet - INFO - Finding fastq/fasta files 2020-02-22 14:44:33,711 - phyluce_assembly_assemblo_velvet - INFO - File type is fastq 2020-02-22 14:44:33,711 - phyluce_assembly_assemblo_velvet - INFO - Running velveth against data 2020-02-22 16:45:56,014 - phyluce_assembly_assemblo_velvet - INFO - Running velvetg against data Traceback (most recent call last): File "/PATH/anaconda3/envs/phyluce/bin/phyluce_assembly_assemblo_velvet", line 259, in main() File "/PATH/anaconda3/envs/phyluce/bin/phyluce_assembly_assemblo_velvet", line 250, in main contigs_file = get_contigs_file_from_output(output) File "/PATH/anaconda3/envs/phyluce/bin/phyluce_assembly_assemblo_velvet", line 185, in get_contigs_file_from_output return glob.glob(os.path.join(output, "contigs.fa"))[0] IndexError: list index out of range

I check the log file, Its nothing there. Main issue is that I run AByss first and works perfect, but ones I start to running the same data with Velvet it fail after assembly correctly one species.

I appreciate all the help you can give me with this issue.

Best, Oscar.