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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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Minimum homopolymer length (msisensor-pro baseline is killed if it is set to 5) #44

Open emesexochitl opened 2 years ago

emesexochitl commented 2 years ago

When I do the scanning on my genome (Hg19) and I set the minimum length of the homopolymer markers to 5, it finishes, but when I try to generate the baseline using this and set the minimum length of homopolymers to 5, it exits with a 'Killed' error message. When I set it to 6, it runs without problems. Could somebody please help me? Many thanks!

Commands I used:

msisensor-pro scan -d ../../../MSI_Data/References/hg19.fa -o MSI_mono_markers.txt -p 1 -l 5 -c 4

msisensor-pro baseline -d MSI_mono_markers.txt -i config_bams.txt -o Baseline/ -g ../../MSI_Data/References/hg19.fa -x 1 -p 5 baseline -d MSI_mono_markers.txt -i config_bams.txt -o Baseline/ -g ../../MSI_Data/References/hg19.fa -x 1 -p 5 Start at: Mon Jun 13 12:50:23 2022

Check for the environment ... Current work path: /home/eso/MSI_Development/MSISensor_Pro/min_5 Microsatellites file: /home/eso/MSI_Development/MSISensor_Pro/min_5/MSI_mono_markers.txt Configure file path: /home/eso/MSI_Development/MSISensor_Pro/min_5/config_bams.txt Output path:/home/eso/MSI_Development/MSISensor_Pro/min_5/Baseline /home/eso/MSI_Development/MSISensor_Pro/min_5/Baseline/ is existing! OK! /home/eso/MSI_Development/MSISensor_Pro/min_5/Baseline/detail is existing! OK!

Load files ... ../../../MSI_Data/Fusion_BAMs/A22-7270_PH21-5216-H22-54_HS2-Lung_BC63_S5_20220320_220855_fusion.bam case1 /home/eso/MSI_Data/Fusion_BAMs/A22-7270_PH21-5216-H22-54_HS2-Lung_BC63_S5_20220320_220855_fusion.bam case1 load bam:/home/eso/MSI_Data/Fusion_BAMs/A22-7270_PH21-5216-H22-54_HS2-Lung_BC63_S5_20220320_220855_fusion.bam OK! ../../../MSI_Data/Fusion_BAMs/A22-7271_PH21-5214-H22-54_HS2-Lung_BC59_S1_20220320_230718_fusion.bam case2 /home/eso/MSI_Data/Fusion_BAMs/A22-7271_PH21-5214-H22-54_HS2-Lung_BC59_S1_20220320_230718_fusion.bam case2 load bam:/home/eso/MSI_Data/Fusion_BAMs/A22-7271_PH21-5214-H22-54_HS2-Lung_BC59_S1_20220320_230718_fusion.bam OK! ../../../MSI_Data/Fusion_BAMs/A22-7272_PH21-5214-H22-54_HS2-Lung_BC60_S2_20220321_000423_fusion.bam case3 /home/eso/MSI_Data/Fusion_BAMs/A22-7272_PH21-5214-H22-54_HS2-Lung_BC60_S2_20220321_000423_fusion.bam case3 load bam:/home/eso/MSI_Data/Fusion_BAMs/A22-7272_PH21-5214-H22-54_HS2-Lung_BC60_S2_20220321_000423_fusion.bam OK! ../../../MSI_Data/Fusion_BAMs/A22-7273_PH21-5214-H22-54_HS2-Lung_BC61_S3_20220321_010253_fusion.bam case4 /home/eso/MSI_Data/Fusion_BAMs/A22-7273_PH21-5214-H22-54_HS2-Lung_BC61_S3_20220321_010253_fusion.bam case4 load bam:/home/eso/MSI_Data/Fusion_BAMs/A22-7273_PH21-5214-H22-54_HS2-Lung_BC61_S3_20220321_010253_fusion.bam OK! ../../../MSI_Data/Fusion_BAMs/A22-7276_PH21-5217-H22-54_HS2-Lung_BC66_S8_20220321_041013_fusion.bam case5 /home/eso/MSI_Data/Fusion_BAMs/A22-7276_PH21-5217-H22-54_HS2-Lung_BC66_S8_20220321_041013_fusion.bam case5 load bam:/home/eso/MSI_Data/Fusion_BAMs/A22-7276_PH21-5217-H22-54_HS2-Lung_BC66_S8_20220321_041013_fusion.bam OK! Loading homopolymer and microsatellite sites ... Killed

PengJia6 commented 1 year ago

Thanks for your questions! I am also confused about this problem! I will check it as soon as possible. 

emesexochitl commented 1 year ago

Thank you so much!