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HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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Exit in environment checking #325

Closed xiaolongliang closed 4 months ago

xiaolongliang commented 4 months ago

Hello, I encountered an issue while running Clair3. Could you please advise me on how to resolve this problem?

[INFO] Check environment variables [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/log [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/pileup_output [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/merge_output [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/phase_output [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/gvcf_tmp_output [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/full_alignment_output [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/phase_output/phase_vcf [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/phase_output/phase_bam [INFO] Create folder /opt/synData2/2024/kazak_sheep/SNP/BH2/tmp/full_alignment_output/candidate_bed [INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default [WARNING] No contig intersection found, output header only in /opt/synData2/2024/kazak_sheep/SNP/BH2/merge_output.vcf.gz [INFO] Exit in environment checking

zhengzhenxian commented 4 months ago

@xiaolongliang

Pls try to enable the --include_all_ctgs option.

xiaolongliang commented 4 months ago

@zhengzhenxian Thanks a lot, it worked!