hapdup tool related error

[dasn588]

Hi, I am getting the following error regarding hapdup program execution:

Finding breakpoints [2023-04-13 11:36:19] INFO: Parsed 3934881 reads 707571 split reads [2023-04-13 11:36:32] INFO: Running: flye-minimap2 -ax asm5 -t 50 -K 5G -I 64G assembly.fasta flye_hap_1/polished_1.fasta 2>/dev/null | flye-samtools sort -m 4G -@4 > structural/liftover_hp1.bam Killed [E::sam_hrecs_error] [E::sam_hrecs_error] [E::sam_hrecs_error] Malformed key:value pair at line 4138: "@SQ SN:contig_9412 L"Malformed key:value pair at line 4138: "@SQ SN:contig_9412 L"Malformed key:value pair at line 4138: "@SQ SN:contig_9412 L"

Please let me know how to resolve the given error.

Thanks Nihar

[mikolmogorov]

Hi Nihar,

This may be caused by samtools version incompatibility: https://github.com/samtools/samtools/issues/1237. Are you using Docker image or manual installation? If manual, you may need to update samtools.

[mikolmogorov]

Hm, now I realize that it's probably something else, since hapdup is using minimap2/samtools packaged with Flye.

I see that minimap2 was killed, this is likely due to running out of memory. What is the size of your genome and how much RAM did you have? Also, nearly-final versions of polished haplotypes should already be available at: flye_hap_1/polished_1.fasta and flye_hap_2/polished_1.fasta

The fastest way to solve the issue on your side would be to run on a machine with larger RAM. I'll try to reduce this requirement in the upcoming versions.

[dasn588]

Hi Mikhail, Thank you for the response. I would like to inform you that I have resolved the query from my end by using different version of Samtools (v1.9). This time I got the final output files.

Thanks Nihar

On Wednesday, April 19, 2023, Mikhail Kolmogorov @.***> wrote:

Hi Nihar,

This may be caused by samtools version incompatibility: samtools/samtools#1237 https://github.com/samtools/samtools/issues/1237. Are you using Docker image or manual installation? If manual, you may need to update samtools.

— Reply to this email directly, view it on GitHub https://github.com/KolmogorovLab/hapdup/issues/28#issuecomment-1514905198, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3B6RFZ6HQMUN7NN7J7TIGTXB75TNANCNFSM6AAAAAAW5BLMT4 . You are receiving this because you authored the thread.Message ID: @.***>

[mikolmogorov]

Good to know, thanks!