error: ".FALSE" ?

[jenny315]

hi, The following screen outputted when I ran the command python pipeline.py --hic-path /public/home/jenny/data/hic/ --pb-path /public/home/jenny/data/ccs/ --sample nl --prefix dip_asm

./pipeline.sh /public/home/jenny/data/hic/ /public/home/jenny/data/ccs/ nl FALSE dip_asm

I'm not sure if this is an error message, I have checked HIC and HIFI data, both of which are FASTQ files and have been decompressed, but there are other files under this path, such as the files before decompression. I can't think of the cause of this mistake

Thanks for any advice, Best regards, Jenny

[shilpagarg]

Please see #16

[jenny315]

Hi, Thank you very much, although I don't quite understand what does it means that dipasm is a proof-of-concept tool .

1.Does this mean that I can also adopt the above idea(hifiasm+pstools) instead of using diPasm? 2.For diploid fish (the haploid genome <1G), can the result of Hifiasm mentioned above be replaced by the result of Hicanu?

Thanks for any advice, Best regards, Jenny

[shilpagarg]

Yes, please use hifiasm+pstools, because it is fast, accurate, as well as user-friendly. In theory, hifiasm and Hicanu graphs should be similar, but I have not yet tested hicanu graphs.

Let me know if you have any questions. Look forward!

[jenny315]

Thank you very much, I'll have a try at once.

Best regards, Jenny

[shilpagarg]

hic_mapping_unitig is a subcommand in pstools. Please read instructions carefully. Thanks.

[duhuipeng]

Thank you

[duhuipeng]

dear author I applied your test data in dipasm, However, he made the mistake and what caused it.

[duhuipeng]

/home/Mpzhang/HpDu/dipasm/DipAsm/hi-c/hic_1.fastq.gz) <(zcat /home/Mpzhang/HpDu/dipasm/DipAsm/hi-c/hic_2.fastq.gz); /home/Mpzhang/Mzhou/Biosoft/pstools resolve_haplotypes -t 64 hic_name_connection.output pgp1.asm.r_utg.gfa ./; /home/Mpzhang/Mzhou/Biosoft/pstools hic_mapping_haplo -t 64 pred_haplotypes.fa <(zcat /home/Mpzhang/HpDu/dipasm/DipAsm/hi-c/hic_1.fastq.gz) <(zcat /home/Mpzhang/HpDu/dipasm/DipAsm/hi-c/hic_2.fastq.gz) -o scaff_connections.txt; /home/Mpzhang/Mzhou/Biosoft/pstools haplotype_scaffold -t 64 scaff_connections.txt pred_haplotypes.fa ./

This is the code I run, the data comes from githup test data, the result is the picture above,Why is this happening

[shilpagarg]

It may be efficient to schedule a meeting. If you could write me at shilpa.garg2k7@gmail.com, that would be good.

[duhuipeng]

ok, I am writing now