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lumpy: a general probabilistic framework for structural variant discovery
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parameter required for mean #383

Open J-Bradlee opened 2 years ago

J-Bradlee commented 2 years ago

Hi there,

Currently running into some issues with lumpy producing a "parameter required mean" error. There are a lot of pair ends being analyzed, however they all have the associated mean parameter. I not sure if this error has to do with the provided histo or bam files, or simply too many pair ends being analyzed. Any insight would be appreciated.

Here is the command:

lumpy -mw 3 -tt 0 -x /app/ref-data/refdata-b38/exclude.cnvnator_100bp.GRCh38.20170403.bed 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-6E4BB213,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-6E4BB213.pe.histo,mean:169,stdev:66,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-78EFC573,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-78EFC573.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-F7D86D9,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-F7D86D9.pe.histo,mean:207,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-195A14DC,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-195A14DC.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-3B931CD3,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-3B931CD3.pe.histo,mean:207,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-751768B7,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-751768B7.pe.histo,mean:209,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-540F8D02,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-540F8D02.pe.histo,mean:209,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1B3349F0,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1B3349F0.pe.histo,mean:213,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-3F258A9,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-3F258A9.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-522D7BAE,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-522D7BAE.pe.histo,mean:177,stdev:54,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-2A2ADCD2,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-2A2ADCD2.pe.histo,mean:214,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-4D8669DE,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-4D8669DE.pe.histo,mean:198,stdev:62,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-4BB1B31E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-4BB1B31E.pe.histo,mean:207,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-8E003D0,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-8E003D0.pe.histo,mean:213,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7EB398D2,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7EB398D2.pe.histo,mean:207,stdev:67,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-40D9B829,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-40D9B829.pe.histo,mean:211,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-173E4E60,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-173E4E60.pe.histo,mean:205,stdev:65,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-45A80D4F,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-45A80D4F.pe.histo,mean:209,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-3E68BEE3,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-3E68BEE3.pe.histo,mean:180,stdev:62,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-73313D72,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-73313D72.pe.histo,mean:206,stdev:66,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-69AAFDC4,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-69AAFDC4.pe.histo,mean:208,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-20DA6124,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-20DA6124.pe.histo,mean:211,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-39D32F8,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-39D32F8.pe.histo,mean:135,stdev:62,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-C8E21EC,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-C8E21EC.pe.histo,mean:208,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-65B3E48D,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-65B3E48D.pe.histo,mean:207,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-2ECB71F3,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-2ECB71F3.pe.histo,mean:200,stdev:64,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-4E2C08F2,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-4E2C08F2.pe.histo,mean:210,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-6B241F5E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-6B241F5E.pe.histo,mean:212,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-18FBBE39,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-18FBBE39.pe.histo,mean:212,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7F253029,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7F253029.pe.histo,mean:193,stdev:61,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-634723B1,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-634723B1.pe.histo,mean:208,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-4B91F693,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-4B91F693.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-15389DE1,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-15389DE1.pe.histo,mean:195,stdev:66,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-6CDECEA,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-6CDECEA.pe.histo,mean:209,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-3E1D60A,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-3E1D60A.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-55830597,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-55830597.pe.histo,mean:210,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-366CEAC2,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-366CEAC2.pe.histo,mean:209,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-2E78A28F,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-2E78A28F.pe.histo,mean:209,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-3BC75783,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-3BC75783.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7D2DD4B,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7D2DD4B.pe.histo,mean:200,stdev:59,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-53FC01A3,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-53FC01A3.pe.histo,mean:157,stdev:65,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-AF10183,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-AF10183.pe.histo,mean:210,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-5F822E06,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-5F822E06.pe.histo,mean:209,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-77F084D6,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-77F084D6.pe.histo,mean:208,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-76D4C2EC,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-76D4C2EC.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-76F0DF82,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-76F0DF82.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
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-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-20E53D1A,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-20E53D1A.pe.histo,mean:207,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-5C9A4182,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-5C9A4182.pe.histo,mean:214,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-2775E119,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-2775E119.pe.histo,mean:213,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-25D6F2B3,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-25D6F2B3.pe.histo,mean:209,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1C89582B,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1C89582B.pe.histo,mean:194,stdev:71,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-DEBFBCE,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-DEBFBCE.pe.histo,mean:197,stdev:64,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1F675481,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1F675481.pe.histo,mean:184,stdev:76,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-525FAFD3,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-525FAFD3.pe.histo,mean:164,stdev:62,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-52AD23E6,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-52AD23E6.pe.histo,mean:202,stdev:67,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1BC1EB3D,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1BC1EB3D.pe.histo,mean:208,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-351554D6,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-351554D6.pe.histo,mean:183,stdev:56,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-F5627E1,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-F5627E1.pe.histo,mean:213,stdev:70,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7B767BC8,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7B767BC8.pe.histo,mean:183,stdev:71,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-4CC6D66E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-4CC6D66E.pe.histo,mean:208,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-9CB851D,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-9CB851D.pe.histo,mean:207,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-22A774E6,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-22A774E6.pe.histo,mean:,stdev:,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-668A24E8,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-668A24E8.pe.histo,mean:209,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-49CFE59C,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-49CFE59C.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7ACEAF1,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7ACEAF1.pe.histo,mean:208,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1BA2F84C,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1BA2F84C.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-CCAB680,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-CCAB680.pe.histo,mean:216,stdev:71,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-6DEF377A,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-6DEF377A.pe.histo,mean:207,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-8E8B0DF,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-8E8B0DF.pe.histo,mean:207,stdev:67,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-369E1A8E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-369E1A8E.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1B48D533,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1B48D533.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7EDE1609,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7EDE1609.pe.histo,mean:208,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-6371A6DC,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-6371A6DC.pe.histo,mean:151,stdev:73,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-5D17FD8D,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-5D17FD8D.pe.histo,mean:209,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-50B6D14,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-50B6D14.pe.histo,mean:201,stdev:66,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-7F092E6F,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-7F092E6F.pe.histo,mean:212,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-2A7B07EE,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-2A7B07EE.pe.histo,mean:203,stdev:71,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-F1F82B7,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-F1F82B7.pe.histo,mean:207,stdev:67,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-5DDAF9ED,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-5DDAF9ED.pe.histo,mean:210,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-2625E39F,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-2625E39F.pe.histo,mean:209,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-C0634A2,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-C0634A2.pe.histo,mean:208,stdev:67,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-D3B989E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-D3B989E.pe.histo,mean:210,stdev:69,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-1D15AFFD,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1D15AFFD.pe.histo,mean:209,stdev:68,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20 
-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-32618E94,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-32618E94.pe.histo,mean:176,stdev:63,read_length:151,min_non_overlap:121,discordant_z:3,back_distance:10,weight:1,min_mapping_threshold:20
-sr id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.splitters.f.bam,back_distance:10,weight:2,min_mapping_threshold:20

Here's the output:

162 0
202 0
94  0
185 0
164 0
196 0
185 0
163 0
197 0
185 0
188 0
41  0
194 0
143 0
203 0
Parameter required for mean

Program: ********** (v 0.2.13)
Author:  Ryan Layer (rl6sf@virginia.edu)
Summary: Find structural variations in various signals.

Usage:   ********** [OPTIONS] 

Options: 
    -g  Genome file (defines chromosome order)
    -e  Show evidence for each call
    -w  File read windows size (default 1000000)
    -mw minimum weight for a call
    -msw    minimum per-sample weight for a call
    -tt trim threshold
    -x  exclude file bed file
    -t  temp file prefix, must be to a writeable directory
    -P  output probability curve for each variant
    -b  output BEDPE instead of VCF
    -sr bam_file:<file name>,
        id:<sample name>,
        back_distance:<distance>,
        min_mapping_threshold:<mapping quality>,
        weight:<sample weight>,
        min_clip:<minimum clip length>,
        read_group:<string>

    -pe bam_file:<file name>,
        id:<sample name>,
        histo_file:<file name>,
        mean:<value>,
        stdev:<value>,
        read_length:<length>,
        min_non_overlap:<length>,
        discordant_z:<z value>,
        back_distance:<distance>,
        min_mapping_threshold:<mapping quality>,
        weight:<sample weight>,
        read_group:<string>

    -bedpe  bedpe_file:<bedpe file>,
        id:<sample name>,
        weight:<sample weight>