invalid argument to stoi

[jthmiller]

Hello, Adding the '--blacklist' opt results in the error below (v1.1.3). I tried the dev branch as well. Any insight is much appreciated. Thanks!

Error-

-----------------------------------------------------------
---  Running svaba SV and indel detection on 12 threads ---
---    (inspect *.log for real-time progress updates)   ---
-----------------------------------------------------------
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoi
Aborted

*.log-

***************************** PARAMS ****************************
    DBSNP Database file: 
    Max cov to assemble: 100
    Error correction mode: f
    Subsample-rate for correction learning: 0.500000
    ErrorRate: EXACT (0)
    Num assembly rounds: 3
    Num reads to sample: 2000000
    Discordant read extract SD cutoff:  3.92
    Discordant cluster std-dev cutoff:  3.92
    Minimum number of reads for mate lookup 3
    LOD cutoff (non-REF):            8
    LOD cutoff (non-REF, at DBSNP):  6
    LOD somatic cutoff:              6
    LOD somatic cutoff (at DBSNP):   10
    BWA-MEM params:
      Gap open penalty: 32
      Gap extension penalty: 1
      Mismatch penalty: 18
      Aligment bandwidth: 1000
      Z-dropoff: 100
      Clip 3 penalty: 5
      Clip 5 penalty: 5
      Reseed trigger: 1.5
      Sequence match score: 2
*****************************************************************

Command-

svaba run \
    -t alignment/$sample.bam \
    -n alignment/$normal.bam \
    -G reference/genome.fa \
    --id-string sv-calls/svaba/wgs/$sample \
    --threads $SLURM_CPUS_PER_TASK \
    -r all 

[walaj]

I wonder if there is a mismatch between the chr names in the blacklist file and the header of the BAM. Svaba uses the BAM header to serves as the LUT between chr name and an associated number — this is often a cause of these sorts of crashes. Especially if early on like this.

If not this, am not sure and would need more info to troubleshoot.

On Nov 24, 2020, at 7:53 AM, Jeffrey Miller notifications@github.com wrote:

 Hello, Adding the '--blacklist' opt results in the error below (v1.1.3). I tried the dev branch as well. Any insight is much appreciated. Thanks!

Error-

---

--- Running svaba SV and indel detection on 12 threads --- --- (inspect *.log for real-time progress updates) ---

terminate called after throwing an instance of 'std::invalid_argument' what(): stoi Aborted *.log-

***** PARAMS **** DBSNP Database file: Max cov to assemble: 100 Error correction mode: f Subsample-rate for correction learning: 0.500000 ErrorRate: EXACT (0) Num assembly rounds: 3 Num reads to sample: 2000000 Discordant read extract SD cutoff: 3.92 Discordant cluster std-dev cutoff: 3.92 Minimum number of reads for mate lookup 3 LOD cutoff (non-REF): 8 LOD cutoff (non-REF, at DBSNP): 6 LOD somatic cutoff: 6 LOD somatic cutoff (at DBSNP): 10 BWA-MEM params: Gap open penalty: 32 Gap extension penalty: 1 Mismatch penalty: 18 Aligment bandwidth: 1000 Z-dropoff: 100 Clip 3 penalty: 5 Clip 5 penalty: 5 Reseed trigger: 1.5 Sequence match score: 2

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[jthmiller]

Thanks for the guidance. This was exactly the case. A reformatted (chr names) and resorted BED file fixed it. Thanks again.