Question: ERROR:PBcR Aborted (terminate called after throwing an instance of 'std::bad_alloc')
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gravatar for 349000955
12 months ago by
3490009550
3490009550 wrote:

Hi all: i assemble a genome size 1.8 Gb with 40X pacbio reads and 30X NGS reads.when the program run at overlapStoreBuild it give a ERROR: Failed with signal ABRT,the program Aborted core dumped and exit.I look into the asm.ovlStore.BUILDING file there is a file about size 2.4 T while other file are about 180Gb.

/software/wgs-8.3rc2/Linux-amd64/bin/PBcR -length 1000 -partitions 200 -libraryname AA2 -threads 50 -genomeSize 1800000000 -s pb.spec -fastq ../00_data/AA2_Pcbio.fastq ../04_data4NGS/flashout/InsertSize_250.notCombined.frg ../04_data4NGS/flashout/InsertSize_346.notCombined.frg ../04_data4NGS/flashout/InsertSize_350.notCombined.frg ../04_data4NGS/flashout/InsertSize_500.notCombined.frg

i use flash to flash the NGS pe reads and use fastq2ca to generate NGS frg.Can you give some suggestion about my question.

pbcr assembly • 395 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 20 • written 12 months ago by 3490009550

Thank you suggestion rhall,but my boss require assemble the genome with NGS data and pacbio data together,and he think it will give a better result with 30X NGS data added.

ADD REPLYlink written 12 months ago by 3490009550

@rhall works at PacBio and it would be wise to heed his advice.
Convince your boss that you want to try @rhall's way first and if that does not work do the thing your boss wants.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax27k

OK,thank you and i will have a try.Also i assembly those pacbio data to generate a genome size 1.45 Gb contig N50 197 kb,will canu have a better result in genome size and N50 compare with falcon?

ADD REPLYlink written 12 months ago by 3490009550

Can't say. You won't know until you try canu.

ADD REPLYlink written 12 months ago by genomax27k
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gravatar for rhall
12 months ago by
rhall150
United States
rhall150 wrote:

I would suggest assembling the 40x pacbio alone (http://canu.readthedocs.io/en/stable/) then using the other data as a validation. The hybrid approach is going to be very compute intensive, and will likely not give any better results.

ADD COMMENTlink written 12 months ago by rhall150
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