Check whether the software is running properly

[duan12345678]

Hi @brentp ,

Thanks for writing this useful tool.
I encountered some issues while running the software. Although there are no obvious errors, the execution speed exceeded my expectations and seems unusually fast. I would like to ask for your guidance on whether this behavior is correct. Below are the commands I used ：
/home/software/smoove-0.2.8/smoove genotype -d -x -p 1 --name 1-10-joint --outdir results-genotyped --fasta genomic.fna --vcf merged.sites.vcf.gz -o 1-10.genotype.bcf 1-10sort.bam
[smoove] 2024/12/23 02:15:29 starting with version 0.2.8
[smoove] 2024/12/23 02:15:29 writing sorted, indexed file to 1-10-LGA_genotype.bcf/1-10-joint-smoove.genotyped.vcf.gz
[smoove] 2024/12/23 02:15:29 > gsort version 0.1.4
[smoove] 2024/12/23 02:21:37 smoove version: 0.1.9

smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.

*[Y] bgzip [ sort -> (compress) -> index ]
*[Y] gsort [(sort) -> compress -> index ]
*[Y] tabix [ sort -> compress -> (index)]
*[Y] lumpy
*[Y] lumpy_filter
*[Y] samtools [only required for CRAM input]

[Y] mosdepth [extra filtering of split and discordant files for better scaling]
[Y] svtyper [required to genotype SV calls]
[Y] svtools [only needed for large cohorts].

Available sub-commands are below. Each can be run with -h for additional help.

call : call lumpy (and optionally svtyper)
merge : merge and sort (using svtools) calls from multiple samples
genotype : parallelize svtyper on an input VCF
paste : square final calls from multiple samples (each with same number of variants)
annotate : annotate a VCF with gene and quality of SV call
2024/12/23 02:21:37 exit status 1
Meanwhile,I also met the error about "panic: runtime error: invalid memory address or nil pointer dereference".I changed the memory up to 200, but is still not work
.
Many thanks in advance.

Best wishes

[brentp]

can you show the full output of your command as it appears?

[duan12345678]

Hello,
thank you for your response. Based on the command line, I have generated the corresponding result files. Below is the content of the files.

Additionally, I have some extra questions. Do you recommend deduplicating the input BAM files using Samtools?At present, the file I entered is near sort, I don't know if this is the reason

Many thanks in advance.

Best wishes