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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Update flye wrapper to 2.9.2 #1299

Open mvdbeek opened 1 year ago

mvdbeek commented 1 year ago

No command line changes upstream.

mvdbeek commented 1 year ago

All failing tests fail because they (seem to) run out of memory:

Job in error state.. tool_id: flye, exit_code: 1, stderr: [2023-03-30 15:18:49] INFO: Starting Flye 2.9.2-b1786
[2023-03-30 15:18:49] INFO: >>>STAGE: configure
[2023-03-30 15:18:49] INFO: Configuring run
[2023-03-30 15:18:49] INFO: Total read length: 1466260
[2023-03-30 15:18:49] INFO: Reads N50/N90: 9054 / 4697
[2023-03-30 15:18:49] INFO: Minimum overlap set to 5000
[2023-03-30 15:18:49] INFO: >>>STAGE: assembly
[2023-03-30 15:18:49] INFO: Assembling disjointigs
[2023-03-30 15:18:49] INFO: Reading sequences
[2023-03-30 15:19:13] ERROR: Looks like the system ran out of memory
[2023-03-30 15:19:13] ERROR: Command '['flye-modules', 'assemble', '--reads', '/tmp/tmpvyh014zh/job_working_directory/000/10/working/input_0.fasta.gz', '--out-asm', '/tmp/tmpvyh014zh/job_working_directory/000/10/working/out_dir/00-assembly/draft_assembly.fasta', '--config', '/usr/local/lib/python3.10/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg', '--log', '/tmp/tmpvyh014zh/job_working_directory/000/10/working/out_dir/flye.log', '--threads', '2', '--min-ovlp', '5000']' died with <Signals.SIGKILL: 9>.
[2023-03-30 15:19:13] ERROR: Pipeline aborted
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