core dumped

[estolle]

Hi

I am trying to run longcallID on a bee dataset, but i am encountering problems (i used the precompiled binaries)

1. Test dataset
   longcallD call -t 8 $F/test_data/chr11_2M.fa $F/test_data/HG002_chr11_ont_test.bam --ont > xHG002_ont_test.vcf
   this works.

2. my data fail (mapping was done with recent ONT data on a high quality reference with winnowmap
   longcallD call -t $CPUs $REF $OUT/$READFILE.sorted.bam --ont -b $OUT/$READFILE.phased.bam > $OUT/$READFILE.vcf
   ==2025/05/23 06:51:02== [INFO] Opening alignment file: $OUT/$READFILE.sorted.bam
   ==2025/05/23 06:51:11== [INFO] Processed 198321 reads.
   corrupted size vs. prev_size
   Aborted (core dumped)

3. rerunning without phased output goes further:
   longcallD call -t 8 $REF $OUT/$READFILE.sorted.bam --ont > $OUT/$READFILE.vcf
   ==2025/05/23 07:25:17== [INFO] Opening alignment file: ./Bombus.lucorum.dorado.sup410.2kbQ90.sorted.bam
   ==2025/05/23 07:25:20== [INFO] Processed 46493 reads.
   ==2025/05/23 07:25:20== [INFO] Output 455 variants to VCF.
   ==2025/05/23 07:25:22== [INFO] Processed 49455 reads.
   ==2025/05/23 07:25:22== [INFO] Output 12 variants to VCF.
   ==2025/05/23 07:25:25== [INFO] Processed 51933 reads.
   ==2025/05/23 07:25:25== [INFO] Output 184 variants to VCF.
   ==2025/05/23 07:25:28== [INFO] Processed 50440 reads.
   ==2025/05/23 07:25:28== [INFO] Output 798 variants to VCF.
   double free or corruption (out)
   Aborted (core dumped)

The bam file seems normal just as any other bam file i am using.

any idea what could cause this?
THanks

[yangao07]

Hi, I did fix several bugs for ont data since pre-v0.04, not sure if you encounter any of them.
I can take a look if you can share your data with me.
Are you able to share the bam with me? Google drive or something else.
You can just collect the first 200000 reads, e.g., samtools view -F2304 YOUR_BAM -h | head -n 200000 | samtools view -b -o debug.bam

[yangao07]

Please try the latest version v0.0.6 see if the error get fixed.