Comments (5)
If your genome is 2.9Gb, you would need hundreds of millions of reads to correct errors. I guess the large genome size and tiny input file triggers some unexpected behavior. This is still a bug. I will look into that. Thanks.
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+1
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Yes, of course my data set is more than 10k reads, that is just a test set. I can't get it to work on my full data set either though. bcf crashed after reading ~809K out of 147M on my 128GB server
bfc: malloc.c:2842: mremap_chunk: Assertion `((size + offset) & (_rtld_global_ro._dl_pagesize - 1)) == 0' failed.
Aborted (core dumped)
If it would be helpful, I could give you access to that file as well. Thanks for looking into the problem!
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I have just fixed it via 14dbe0f. This is an out-of-boundary bug only showing to read lengths smaller but close to 64bp, 128bp, 256bp, etc. My previous guess was wrong. Many thanks for this example.
I am closing the issue. You can reopen it if the latest master branch does not work.
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I should add that bfc -s 2.9g -k 55 -t 31 smaller.fq
should also work. The segfault is not caused by -s 2.9g
.
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Related Issues (16)
- bfc with MiSeq data? HOT 2
- phred33 to 64 encoding change
- Segfault HOT 10
- Provide summary information
- Document the meaning of -R (refine error-corrected reads)
- How does bfc assign quality scores? HOT 3
- Segmentation fault HOT 5
- BFC-ht versus BFC-bf HOT 1
- Read counter not incrementing HOT 3
- Memory consuming HOT 1
- code for arXiv evaluation table HOT 3
- drop reads containing specific set of kmers HOT 2
- Please tag a new stable release HOT 2
- bfc strips pairing info HOT 6
- Description of output header HOT 5
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