Hi, thanks for this software. I used it on a directory of Nanopore fastq files and it worked beautifully. But when running on a directory of PacBio fastq files I keep getting an error. This error is a variation on what has been reported before but so far I'm unable to overcome it.
Here's the error:
Activating conda environment: ../../../code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/conda/308674b41518b3abe7fb1010240eff8c_
[Thu Oct 17 16:43:56 2024]
Error in rule plassembler_long:
jobid: 171
input: /output/processing/kmc/JM109/JM109_kmcLOG.txt, /output/processing/qc/JM109_filt_trim.fastq.gz
output: /output/processing/plassembler/JM109/plassembler_plasmids.fasta, /output/processing/plassembler/JM109/plassembler_summary.tsv, /output/versions/JM109/plassembler.version
log: /output/stderr/plassembler_long/JM109.log (check log file(s) for error details)
conda-env: /code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/conda/308674b41518b3abe7fb1010240eff8c_
shell:
plassembler long -l /output/processing/qc/JM109_filt_trim.fastq.gz -o /output/processing/plassembler/JM109 -d /code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/../databases -t 16 -c 4000000 --skip_qc --flye_directory /output/processing/assemblies/JM109 --depth_filter 0.25 -f 2> /output/stderr/plassembler_long/JM109.log
touch /output/processing/plassembler/JM109/plassembler_plasmids.fasta
touch /output/processing/plassembler/JM109/plassembler_summary.tsv
plassembler --version > /output/versions/JM109/plassembler.version
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile /output/stderr/plassembler_long/JM109.log:
================================================================================
2024-10-17 16:43:56.623 | INFO | plassembler:begin_plassembler:100 - You are using Plassembler version 1.6.2
2024-10-17 16:43:56.623 | INFO | plassembler:begin_plassembler:101 - Repository homepage is https://github.com/gbouras13/plassembler
2024-10-17 16:43:56.623 | INFO | plassembler:begin_plassembler:102 - Written by George Bouras: george.bouras@adelaide.edu.au
2024-10-17 16:43:56.623 | INFO | plassembler:long:1294 - Database directory is /code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/../databases
2024-10-17 16:43:56.623 | INFO | plassembler:long:1295 - Longreads file is /output/processing/qc/JM109_filt_trim.fastq.gz
2024-10-17 16:43:56.623 | INFO | plassembler:long:1296 - Chromosome length threshold is 4000000
2024-10-17 16:43:56.623 | INFO | plassembler:long:1297 - Output directory is /output/processing/plassembler/JM109
2024-10-17 16:43:56.623 | INFO | plassembler:long:1298 - Min long read length is 500
2024-10-17 16:43:56.623 | INFO | plassembler:long:1299 - Min long read quality is 9
2024-10-17 16:43:56.623 | INFO | plassembler:long:1300 - Thread count is 16
2024-10-17 16:43:56.623 | INFO | plassembler:long:1301 - --force is True
2024-10-17 16:43:56.624 | INFO | plassembler:long:1302 - --skip_qc is True
2024-10-17 16:43:56.624 | INFO | plassembler:long:1303 - --raw_flag is False
2024-10-17 16:43:56.624 | INFO | plassembler:long:1304 - --pacbio_model is nothing
2024-10-17 16:43:56.624 | INFO | plassembler:long:1305 - --keep_chromosome is False
2024-10-17 16:43:56.624 | INFO | plassembler:long:1306 - --flye_directory is /output/processing/assemblies/JM109
2024-10-17 16:43:56.624 | INFO | plassembler:long:1307 - --flye_assembly is nothing
2024-10-17 16:43:56.624 | INFO | plassembler:long:1308 - --flye_info is nothing
2024-10-17 16:43:56.624 | INFO | plassembler:long:1309 - --corrected_error_rate is 0.12
2024-10-17 16:43:56.624 | INFO | plassembler:long:1310 - --no_chromosome is False
2024-10-17 16:43:56.624 | INFO | plassembler:long:1311 - --depth_filter is 0.25
2024-10-17 16:43:56.624 | INFO | plassembler:long:1312 - --unicycler_options is None
2024-10-17 16:43:56.624 | INFO | plassembler:long:1313 - --spades_options is None
2024-10-17 16:43:56.624 | INFO | plassembler:long:1317 - Checking dependencies
2024-10-17 16:43:56.697 | INFO | plassembler.utils.input_commands:check_dependencies:199 - Flye version found is v2.9.5-b1801.
2024-10-17 16:43:56.698 | INFO | plassembler.utils.input_commands:check_dependencies:209 - Flye version is ok.
2024-10-17 16:43:56.705 | INFO | plassembler.utils.input_commands:check_dependencies:218 - Raven v1.8.3 found.
2024-10-17 16:43:56.705 | INFO | plassembler.utils.input_commands:check_dependencies:220 - Raven version is ok.
2024-10-17 16:43:56.772 | ERROR | plassembler.utils.input_commands:check_dependencies:239 - Unicycler not found. Please re-install Unicycler, see instructions at https://github.com/gbouras13/plassembler.
================================================================================
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-10-17T162626.887003.snakemake.log
WorkflowError:
At least one job did not complete successfully.
[2024:10:17 16:43:56] ERROR: Snakemake failed
However, when activate the /code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/conda/308674b41518b3abe7fb1010240eff8c_ conda environment, Unicycler is most definitely installed. Curiously, when I directly run the command from the terminal:
plassembler long -l /output/processing/qc/JM109_filt_trim.fastq.gz -o /output/processing/plassembler/JM109 -d /code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/../databases -t 16 -c 4000000 --skip_qc --flye_directory /output/processing/assemblies/JM109 --depth_filter 0.25 -f 2> /output/stderr/plassembler_long/JM109.log
touch /output/processing/plassembler/JM109/plassembler_plasmids.fasta
touch /output/processing/plassembler/JM109/plassembler_summary.tsv
plassembler --version > /output/versions/JM109/plassembler.version
it appears to complete without error. I tried editing the plasassembler.yaml file as suggested here but this did not solve the problem. I installed everything according to the instructions and as I said, everything worked beautifully the first time. I'm just not sure how to continue from here and any help will be appreciated.
Many thanks!
Hi, thanks for this software. I used it on a directory of Nanopore fastq files and it worked beautifully. But when running on a directory of PacBio fastq files I keep getting an error. This error is a variation on what has been reported before but so far I'm unable to overcome it.
Here's the error:
However, when activate the
/code/conda_envs/hybracterENV/lib/python3.12/site-packages/hybracter/workflow/conda/308674b41518b3abe7fb1010240eff8c_conda environment, Unicycler is most definitely installed. Curiously, when I directly run the command from the terminal:it appears to complete without error. I tried editing the
plasassembler.yamlfile as suggested here but this did not solve the problem. I installed everything according to the instructions and as I said, everything worked beautifully the first time. I'm just not sure how to continue from here and any help will be appreciated.Many thanks!