Comments (4)
I have the same errors with the test data set
miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa
[M::main] ===> Step 1: reading read mappings <===
Segmentation fault (core dumped)
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Me too isovic/racon#22 (comment)
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Hello
I am having a similar issue.
I was mapping data with minimap (0.2.r124.dirty) and tried next to assemble.
The mapping file size is 457 GB and the machine has > 500GB RAM.
Using miniasm (0.2.r137.dirty) it gives a segmentation fault in step 1.
I updated miniasm (0.2.r159.dirty) but still got the same core dump.
This time I monitored as well closely the RAM consumption and it did not exceed 50% of the RAM
at crush-time.
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Hi
No real fix but work-around which was acceptable in my case:
miniasm -Rc2 -f MyReads.fastq.gz MyAlignments.paf.gz > MyAssembly.gfa
This filters contained reads first, which reduced the RAM usage a lot - takes a moment though.
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Related Issues (20)
- how to calculated identity? HOT 1
- No output in GFA file after miniasm run. HOT 4
- Explanation of GFA file format HOT 1
- PAF end coordinates HOT 2
- Segmentation fault (core dumped) while running miniasm HOT 1
- Can miniasm be used for contigs HOT 1
- Hello there, HOT 3
- Number of rounds for short overlap removal
- miniasm prints no gfa if PAF file contains self-mapped read HOT 3
- Conceptual Question About Miniasm
- Empty gfa file after miniasm run HOT 4
- Decreasing minimum required read coverage for assembly
- Miniasm killed process
- PAF Format detail HOT 1
- Not results generating? HOT 5
- Empty paf file. No error message.
- The main disadvantages of Miniasm compared to more modern assemblers
- combine replicates
- Assemble of DNA and RNA amplicons from PacBio run HOT 1
- Next Step after generating assembly.gfa file.
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