Comments (2)
I tested the prlHashReads.c, and found the "openNextFile" function returns 0, and thus it didn't read any fastq files. I'm not sure if it's about some problem in my fastq files, but the fastq files can pass fastqc normally.
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I got it, it's related to "asm_flags" in the config file, I originally set it as 2 because I only want to assemble the scaffold but not contig, and then I met the problem I mentioned above. When I set it as 3, all the thing goes normally. so I guess the scaffold should be run after contig, it's a successive process but not a selection.
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Related Issues (20)
- Dealing graph with too many edges HOT 1
- Empty fastq input results in infinite "air_return error" loop HOT 1
- operation HOT 6
- GapCloser: Segmentation fault (core dumped) HOT 1
- final link failed: Nonrepresentable section on output HOT 1
- soapaligner is not working HOT 5
- not resolved gaps of 1 nucleotide HOT 1
- Are the new releases really new releases? HOT 1
- question about the output file .scafSeq file when using SOAPdenovo2
- Getting the following Error during SOAPdenovo installation
- Ran out of memory while applying -64982367872bytes
- compilation from source failed on debian11, gcc11.2 - patch added
- Negative number of edges in pregraph
- SOAPdenovo2 installation error HOT 3
- SOAPdenovo parameter -K
- cgroup out-of-memory handler
- Using a compressed file during the "pregraph" process may lead to program exit
- Challenges with Scaffold Statistics in SOAPdenovo2 Assembly: Number_of_contigs_in_scaffolds
- cannot open *.kmerFreq file after pregraph, then exit
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