ERROR: fastq is too long. Max acceptable length is 1000000.

[DayTimeMouse]

Hi,

During the simulation of ultra-long ONT reads, an error was encountered: "fastq is too long. Max acceptable length is 1000000."

Will the program be updated?

Best.

[yukiteruono]

Thank you for using PBSIM3. Please increase the value in line 27 (#define FASTQ_LEN_MAX 1000000) of pbsim.cpp and then try make again. PBSIM3 uses more memory, but works fine.

[DayTimeMouse]

Hi yukiteruono,

Thanks for your help, PBSIM3 works now.

I have another questions: To generate HiFi/ONT reads, I intend to use the sample mode, using a sample fastq file containing HiFi reads or ONT reads.

The command: pbsim --strategy wgs --method sample --sample hifi_reads.fastq --depth 30 --genome genome.fa pbsim --strategy wgs --method sample --sample ont_reads.fastq --depth 30 --genome genome.fa

Can the above command get hifi or ont reads?

Best.

[yukiteruono]

ONT reads can be simulated with your command. For HiFi reads, the process of generating consensus reads using ccs software from multi-pass sequencing data is important, so model-based simulation is recommended.

[DayTimeMouse]

After sample-based simulation，then using ccs software to generate HiFi reads，this approach is recommended?

[yukiteruono]

The ccs input must be CLR read multi-pass sequencing, but in PBSIM3, CLR read multi-pass sequencing cannot be done by sample-based simulation (see README). Use model-based simulation for multi-pass sequencing of CLR reads.