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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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free(): invalid next size (fast) at "Simplifying the graph" #684

Closed grinning-bat closed 2 months ago

grinning-bat commented 3 months ago

Hello! I have another assembly which crashed. version:

[2024-03-05 16:24:22] root: INFO: Starting Flye 2.9.3-b1797
[2024-03-05 16:24:22] root: DEBUG: Cmd: [redacted]/verkko/env/bin/flye --threads 63 --nano-raw [redacted]_all_pass.fastq.gz --out-dir [redacted] 
[2024-03-05 16:24:22] root: DEBUG: Python version: 3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:33:10) 
[GCC 12.3.0]

[2024-03-12 15:13:16] INFO: Simplifying the graph
free(): invalid next size (fast)
[2024-03-12 15:56:40] ERROR: Command '['flye-modules', 'repeat', '--disjointigs', '[redacted]/10-consensus/consensus.fasta', '--reads', '[redacted]_all_pass.fastq.gz', '--out-dir', '[redacted]/20-repeat', '--config', '[redacted]/env/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg', '--log', '[redacted]/flye.log', '--threads', '63', '--min-ovlp', '4000']' died with .
[2024-03-12 15:56:40] ERROR: Pipeline aborted

flye.log:

[2024-03-12 15:56:18] DEBUG: Peak RAM usage: 225 Gb
[2024-03-12 15:56:40] root: ERROR: Command '['flye-modules', 'repeat', '--disjointigs', '[redacted]/10-consensus/consensus.fasta', '--reads', '[redacted]_all_pass.fastq.gz', '--out-dir', '[redacted]/20-repeat', '--config', '[redacted]/env/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg', '--log', '[redacted]/flye.log', '--threads', '63', '--min-ovlp', '4000']' died with .
[2024-03-12 15:56:40] root: ERROR: Pipeline aborted

Please tell which additional info (input files, full logs, debug traces) you need and how to collect it.

WBR

mikolmogorov commented 3 months ago

Is it the same run from #682 ? If so, it means it progressed? Please see my questions in the other thread. And uploading the full flye.log will be helpful too.

grinning-bat commented 3 months ago

Hello. It's different run and different dataset. I have several species of one group with varying genome sizes/repeat content. Now I'm running flye-modules with parameters from "ERROR: Command" line under gdb to get a stack trace.

Log of a previous run attached: flye_redacted.log.zip

mikolmogorov commented 3 months ago

Thanks, and sorry for the late response! According to the log, program basically finished, but likely some memory inconsistency was revealed during the cleanup. You should be able to continue run by adding --resume-from polishing option.

Did gdb end up producing a stack trace? Is the crash reproducible? Did you compile from source (and if not, can you try and see if crash still occurs?)

mikolmogorov commented 2 months ago

Closed due to inactivity, feel free to reopen if you still need help with this.