Comments (8)
a sample of the nanopore reads
nanopore_test.txt
from spades.
Is there any possibility for you to share your data with us so we could reproduce and fix an issue?
from spades.
The data are here
https://drive.google.com/open?id=0B4JUBQuE6tBCSnRtV1F0RmlnRzQ
The assembly completes when using a subset of the HiSeq reads, up to about 10M paired end reads
8-core MacPro with 128Gb RAM
from spades.
Thanks, we downloaded all the files. Which nanopore reads you used? B5_all or B5_qs10? Your params.txt indicates that you used "B5.correctedReads_rename.fasta.gz"
from spades.
from spades.
any ideas?
from spades.
We introduced some changes and the problem should be fixed in SPAdes 3.11
from spades.
Fixed in 3.11
from spades.
Related Issues (20)
- Incompatible licenses HOT 1
- Error == system call for: config.info HOT 4
- Spades finished abnormally HOT 1
- SPAdes: Running since 4 days HOT 4
- Resuming Hybrid Assembly fails HOT 2
- OS return value: -9 HOT 5
- == Error == system call for: spades-core, finished abnormally, OS return value: -9 HOT 1
- Linux build does not run in a directory containing spaces
- Input requirement for hybrid assembly HOT 6
- error while parsing GFA path record HOT 7
- ERROR HOT 5
- Error-6 can not open tmp folder HOT 1
- core dump when runing pathracer HOT 2
- Error code 2. unlink(2) failed HOT 1
- == Error == system call for: finished abnormally, OS return value: 21 (Pair of read files contain unequal amount of reads) HOT 8
- sequence name is empty HOT 3
- Minority mutations used for final assembly (metaspades, hybrid ONT-SR) HOT 2
- spades-core: /spades/assembler/src/common/assembly_graph/core/debruijn_data.hpp:38: void debruijn_graph::CoverageData::inc_coverage(int): Assertion `value >= 0 || coverage_ > unsigned(-value)' failed. HOT 1
- spades 4.0.0 mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 HOT 5
- Files with merged reads were ignored HOT 6
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from spades.