decodegenetics / lrcaller Goto Github PK

Hi, we tried this software but got an error that:
terminate called after throwing an instance of 'seqan::EmptyFieldError'
what(): GENOTYPE_3 field was empty.
/opt/gridview//pbs/dispatcher/mom_priv/jobs/537340.admin1.SC: line 31: 99338 Aborted

LRcaller was with the following settings:
LRcaller -fa ${fasta} -nt $threads -a minimap ${bam} ${sv} ${sv_geno}

Do you know how to deal with this problem?
Thank you very much

Hi there,
I encountered an installation error, algo.hpp does not have ”viewRecords“ function, how can I get this function?
The error message is：
LRcaller/algo.hpp:1126:13: error: ‘viewRecords’ was not declared in this scope; did you mean ‘vcfRecords’?
1126 | viewRecords(bars, bamFiles[i], bamIndexes[i], bamRID, genome_begin, genome_end);
| ^~~~~~~~~~~

All the best,
YU

Hi,

We run into erros (std::bad_alloc) while trying to run LRcaller with the following settings:

tools/LRcaller -nt 5 /mnt/SCRATCH/kristenl/Alignments/Barry_to_Simon.bam /mnt/SCRATCH/kristenl/SV_calling/SVIM/Barry_to_Simon/Barry_to_Simon_SVIM_q10.vcf test.vcf -v

Verbose:
LRcaller_out.txt

Do you have any suggestions on how to fix this?

Thanks

Hi
It occurs the error messgae of "Parameter regionStart was greater than regionEnd" when I run LRcaller. I checked the SVs in the input vcf file, and did not found SVs whose start position is greater than end position. So could you please give me some suggestions to debug the error? or display the specific SV that cause the error message? In addition, the SV calls in the input vcf file are generated by cuteSV, and are merged by Jasmine. The versison of LRcaller I used is v1.0.

Thanks in advance
Jiao

Dear LRcaller team,

I am calling SV genotypes on a dataset of 20 individuals sequenced with ONT (~40X).
I am runing LRcaller in parallel on each chromosome.

LRcaller help indicates that 3 different aligners can be used : bwa, minimap2 or seqan.
Using seqan, works perfectly, but requires a substantial amount of computing time.
Would one of the other aligner be a solution if I am facing a computing time issue ?

Thank you in advance for your help.

Regards,
Thomas

Hi there,

I tried to build LRcaller using the instruction but failed to do so,

remote: Total 170 (delta 78), reused 148 (delta 66), pack-reused 0
Receiving objects: 100% (170/170), 5.55 MiB | 1.04 MiB/s, done.
Resolving deltas: 100% (78/78), done.
Submodule 'submodules/seqan' ([email protected]:seqan/seqan.git) registered for path 'submodules/seqan'
Cloning into 'submodules/seqan'...
Warning: Permanently added the RSA host key for IP address '13.236.229.21' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Clone of '[email protected]:seqan/seqan.git' into submodule path 'submodules/seqan' failed

It seems that seqan is now moved

ATTENTION: SeqAn3 is out and hosted in a different repository: https://github.com/seqan/seqan3
--
All new applications should be based on SeqAn3 and all existing applications that receive updates should be ported.

Thanks,

Tuan