Comments (3)
Hi, I'm having the same issue. I'm rerunning a job that worked successfully in July, but is now failing to get past the very first step in Miniasm ([M::main] ===> Step 1: reading read mappings <===). Any help with this issue would be greatly appreciated.
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Hi, I'm having this issue too, where Miniasm stops at step 1. Seems that many have this issue, but no one really have a solution. Some say it is a problem in the self-mapping process. If anyone can help with this problem, I (and my lab) would appreciate it.
from miniasm.
The weird thing for me is that I've successfully run this exact assembly before. This is what I'm doing:
minimap2 -x ava-ont -r 10000 -t 16 reads.fastq.gz reads.fastq.gz > overlap.paf
miniasm reads.fastq.gz overlap.paf.gz > reads.gfa
The only insight I have is that my .paf file generated from minimap2 is different from before and I don't know what I did differently. About 6 months ago, my .paf file was only 1,631.2 GB, but when I run the same code with the same reads I get a .paf file that is 3,498.7 GB. I'm thinking that my issue is stemming from minimap2 and not miniasm. If either of you have found a solution to this, I would appreciate your insight.
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Related Issues (20)
- 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
- 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.
- Minidot invalid option -- 'D'
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