voutcn
commented
10 years ago Hi Alex,
You command line is correct. MEGAHIT accept fasta or fastq file as input. The program crashed because of insufficient memory. In the command line, the -m option was set to be 60000000000 (~56GB). Make sure you have enough memory. You may try a smaller number for the -m option.
Regards, Dinghua
On 1 Oct, 2014, at 12:06 am, Alex Copeland notifications@github.com wrote:
Hi,
I cloned the repo and built megahit without problems, but am having some trouble getting a test run to complete (start) without errors. It's not quite clear from the docs if you require or support fasta, fastq, and/or fastq.gz so I've tried both fastq and fasta as follows:
python ../megahit -r uazx.sample.fa -m 60000000000 -l 150
Which produces the following error
Number of CPU threads 32 [Tue Sep 30 09:03:47 2014]: Extracting solid (k+1)-mers for k = 21 sdbg_builder_cpu: cx1_functions.cpp:192: void phase1::ReadInputFile(global_data_t&): Assertion `packed_reads != __null' failed. Error occurs when running "builder count"
Can you advise me on a correct command line and any specific input requirements e.g. paired, interleaved, fasta, etc. ? Thanks in advance.
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accopeland
Hi,
I cloned the repo and built megahit without problems, but am having some trouble getting a test run to complete (start) without errors. It's not quite clear from the docs if you require or support fasta, fastq, and/or fastq.gz so I've tried both fastq and fasta as follows:
Which produces the following error
Number of CPU threads 32 [Tue Sep 30 09:03:47 2014]: Extracting solid (k+1)-mers for k = 21 sdbg_builder_cpu: cx1_functions.cpp:192: void phase1::ReadInputFile(global_data_t&): Assertion `packed_reads != __null' failed. Error occurs when running "builder count"
Can you advise me on a correct command line and any specific input requirements e.g. paired, interleaved, fasta, etc. ? Thanks in advance.