UnifiedGenotyper always give BGZF file has invalid uncompressedLength: -1792842732

RduqueRduque Posts: 7Member


I running a pipline for exome data. I have 7 exome samples. When the pipeline arrive at the UnifiedGenotyper i always get the error my bam files are malformed.

MESSAGE: SAM/BAM file /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261951.recal.bam is malformed: BGZF file has invalid uncompressedLength: -1792842732

All the bam files have are serveral GB big. So I do not get i why the uncompressed length is negative. Here is what is executed:

java -Xmx8g -jar /lib/gatk/GenomeAnalysisTK-2.1-13-g1706365/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /tmp/db99fcb54f49eea7ce46ff16a802f7ac/human_g1k_v37.fasta -nt 30 -glm BOTH -A AlleleBalance -A DepthOfCoverage -A FisherStrand -D /tmp/db99fcb54f49eea7ce46ff16a802f7ac/dbsnp_135.b37.vcf -o samples.variants.raw.vcf -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261951.recal.bam -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261953.recal.bam -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261952.recal.bam -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261954.recal.bam -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261950.recal.bam -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261955.recal.bam -I /tmp/db99fcb54f49eea7ce46ff16a802f7ac/ISDBM261956.recal.bam




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