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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Having issue at Assert(idx) for msi tumor/normal #57

Closed shivUSF closed 12 months ago

shivUSF commented 1 year ago

Hello, I am using msisensor-pro msi command for tumor/normal paired sample [command mentioned below] However i am again and again running in this error. Initially I thought there is some sort of path error but the paths seems file for tumor normal bam files. Does it need any other file along with the bam file?

Error ----- loading bed regions ... loading homopolymer and microsatellite sites ...

Total loading windows: 2893

Total loading homopolymer and microsatellites: 18252

" [E::idx_find_and_load] Could not retrieve index file for '/mnt/cancergenomics/CCB/gastric_rna_ikl/variant_dna/220300000233-D01/alignment/220300000233-D01_realigned.bam' msisensor-pro: bamreader.cpp:187: bool ReadInBamReads(const char*, const string&, unsigned int, unsigned int, std::vector&, std::string): Assertion `idx' failed. " msisenssor2.sh: line 4: 1266786 Aborted
(core dumped) msisensor-pro msi -d /mnt/cancergenomics/aws_ebs/ikmb_gastric/b37decoy.miscrosatellites.list -t /mnt/cancergenomics/CCB/gastric_rna_ikl/variant_dna/220300000233-D01/alignment/220300000233-D01_realigned.bam -n /mnt/cancergenomics/CCB/gastric_rna_ikl/variant_dna/220300000233-D01/alignment/220300000233-F01_realigned_sorted.bam -e /mnt/cancergenomics/aws_ebs/database/avera/xgen_exome_nochr_6_sorted.bed -o /mnt/cancergenomics/CCB/gastric_rna_ikl/variant_dna/220300000233-D01/report/220300000233-D01.msi

PengJia6 commented 1 year ago

Did you have bam index file along with you bam file? If not, please generated with following scripts: 

samtools index xxxx.bam