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FredHutch / Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
MIT License
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error for gatk PathSeqPipelineSpark "java: bwa.c:329: bwa_mem2idx: Assertion `k == l_mem' failed." #18

Closed leogg738 closed 10 months ago

leogg738 commented 10 months ago

When I run this code gatk --java-options "-Xmx150g" PathSeqPipelineSpark \ --input endometriosis.bam \ --filter-bwa-image pathseq_host.fa.img \ --kmer-file pathseq_host.bfi \ --min-clipped-read-length 60 \ --microbe-fasta pathseq_microbe.fa \ --microbe-bwa-image pathseq_microbe.fa.img \ --taxonomy-file pathseq_taxonomy.db \ --output endometriosis.pathseq.complete.bam \ --scores-output endometriosis.pathseq.complete.csv \ --is-host-aligned false \ --filter-duplicates false \ --min-score-identity .7

The following error message will appear： java: bwa.c:329: bwa_mem2idx: Assertion `k == l_mem' failed. Due to the log is too long, I can't paste all.

I don't know what caused this, and no one has raised similar questions. Please help me.

hanruiw commented 10 months ago

Dear leogg738,

Thank you for your interest in our paper, we have never seen this error before in our analysis, I would recommend you ask GATK team for help. Good luck with your analysis!

Best regards, Hanrui