Crash soon after started

[huanglu2018]

I aligned my RNAseq data using STAR, and ran GangSTR with default settings, which resulted an error as follows:

[GangSTR-2.4] ProgressMeter: Loading read group id g1 for sample s1
[GangSTR-2.4] ProgressMeter: Processing chr1:14070
[GangSTR-2.4] ProgressMeter:    Genotyper Results:  3, 3    likelihood = 9.24477
[GangSTR-2.4] ProgressMeter: Processing chr1:16620
....
[GangSTR-2.4] ProgressMeter: Processing chr1:948423
[GangSTR-2.4] ProgressMeter:    Genotyper Results:  1, 1    likelihood = -25
[GangSTR-2.4] ProgressMeter: Processing chr1:948930
[GangSTR-2.4] ERROR: Invalid CIGAR option encountered in TrimAlignment

when I use a bwa-aligned bam file, the error message disappeared. so this might be caused by the aligner. my STAR options are:

STAR --genomeDir $star_genome_dir \
--readFilesIn $fq1 $fq2 \
--runThreadN $threads \
--limitBAMsortRAM 0 \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix $outdir \
--outFilterMultimapScoreRange 1 \
--outFilterMultimapNmax 20 \
--outFilterMismatchNmax 10 \
--alignIntronMax 500000 \
--alignMatesGapMax 1000000 \
--sjdbScore 2 \
--alignSJDBoverhangMin 1 \
--genomeLoad NoSharedMemory \
--outFilterMatchNminOverLread 0.33 \
--outFilterScoreMinOverLread 0.33 \
--sjdbOverhang 100 \
--outSAMstrandField intronMotif \
--outSAMattributes NM MD MC AS XS \
--outSAMunmapped Within \
--outTmpDir $tmp_dir \
--outSAMattrRGline ID:$id LB:$id SM:$id PL:Illumina PU:$id

Is there a way to use STAR-aligned bam as input?

[nmmsv]

Apologies for my late response! Currently, GangSTR only supports DNA sequencing data (preferably PCR-free whole genome sequencing). RNA seq includes large gaps in alignment that our software does not support. Please reopen this issue if you had any other questions. Thanks! Nima