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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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exist status 256 in lumpy.caller.joined #35

Open jezdip1 opened 2 years ago

jezdip1 commented 2 years ago

hello, I am trying to run your docker image for clinsv1.0. following the steps in https://github.com/KCCG/ClinSV for docker with the sample NA12878_b38, all works fine. when I tried my .bam and .bai data, prepared and referenced to GRCh38 using nf-core/sarek pipeline, the docker instance stops at this step OK # job bigwig, createWigs, MCD1319_2009KNO ran successfully (exit=0) -> skip : /app/project_folder/alignments/MCD1319_2009KNO/bw/sh/bigwig.createWigs.MCD1319_2009KNO.sh

OK # job bigwig, q0, MCD1319_2009KNO ran successfully (exit=0) -> skip : /app/project_folder/alignments/MCD1319_2009KNO/bw/sh/bigwig.q0.MCD1319_2009KNO.sh

OK # job bigwig, q20, MCD1319_2009KNO ran successfully (exit=0) -> skip : /app/project_folder/alignments/MCD1319_2009KNO/bw/sh/bigwig.q20.MCD1319_2009KNO.sh

OK # job bigwig, mq, MCD1319_2009KNO ran successfully (exit=0) -> skip : /app/project_folder/alignments/MCD1319_2009KNO/bw/sh/bigwig.mq.MCD1319_2009KNO.sh

OK # job lumpy, preproc, MCD1319_2009KNO ran successfully (exit=0) -> skip : /app/project_folder/SVs/MCD1319_2009KNO/lumpy/sh/lumpy.preproc.MCD1319_2009KNO.sh

executing: sh /app/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.sh &> /app/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.e ...

finished after (hh:mm:ss): 03:15:18

exist status: 256

***** error exist status != 0 (256), please check /app/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.e for more information

the corresponding *.e file says something about "Parameter required for mean" seems to me, there is a parsing error or something similar

lumpy.caller.joined.e.gz

can you please have a look and tell me what I am doing wrong? or how could I move forward?

J-Bradlee commented 2 years ago

Hi I'm noticing you are receiving an "The index file is older than the data file:" warning from samtools, should be fine if you are sure that bai indexes are up to date. Just checking if you're sure they are up to date.

I had a look at that lumpy command generated I can't see anything wrong with it. All of the -pe arguments has a mean parameter associated...

jezdip1 commented 2 years ago

Thanks for reply, Yes I noticed the Bai date too. But it should be ok. For any other operations I do with these files it is ok. Just for sure Ill double check it again P.

⁣Stáhnout BlueMail pro Android ​

    1. 2022 10:03, 10:03, James Bradley @.***> napsal/a:

      Hi I'm noticing you are receiving an "The index file is older than the data file:" warning from samtools, should be fine if you are sure that bai indexes are up to date. Just checking if you're sure they are up to date.

      I had a look at that lumpy command generated I can't see anything wrong with it. All of the -pe arguments has a mean parameter associated...

      -- Reply to this email directly or view it on GitHub: https://github.com/KCCG/ClinSV/issues/35#issuecomment-1177224036 You are receiving this because you authored the thread.

      Message ID: @.***>

jezdip1 commented 1 year ago

ok, I rechecked and reindexed again the *.bam using samtools, so the bai is really up to date. The new one is actually the same as the previous. And again the same error appeared. Any idea?

lumpy.caller.joined.e.gz

J-Bradlee commented 1 year ago 
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 
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-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-96BEB9E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-96BEB9E.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_M1-533119BA,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-533119BA.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_M1-1666F28C,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1666F28C.pe.histo,mean:206,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_M1-1C3FD523,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1C3FD523.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_M1-1182291E,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-1182291E.pe.histo,mean:182,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_M1-54EE420,histo_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/1234N_M1-54EE420.pe.histo,mean:206,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_M1-20E53D1A,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

I think there might be an issue with lumpy, from this output I can see that the mean parameter is associated correctly. There are a lot of pairends given, so perhaps lumpy can't handle that many. I'll start an issue in the lumpy repo with this and see if we can get any support over there.

J-Bradlee commented 1 year ago 
lumpy -mw 3 -tt 0 -x /app/ref-data/refdata-b38/exclude.cnvnator_100bp.GRCh38.20170403.bed 
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-pe id:MCD1319_2009KNO,bam_file:/app/project_folder/SVs/MCD1319_2009KNO/lumpy/MCD1319_2009KNO.discordants.bam,read_group:1234N_M1-5C9A4182,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

I think there might be an issue with lumpy, from this output I can see that the mean parameter is associated correctly. There are a lot of pairends given, so perhaps lumpy can't handle that many. I'll start an issue in the lumpy repo with this and see if we can get any support over there .

jezdip1 commented 1 year ago

excellent, thank you meanwhile I could perhaps split the bam and see whether the pipeline works P.

On 15.07.22 9:24, James Bradley @.***> wrote:

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 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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

I think there might be an issue with lumpy, from this output I can see that the mean parameter is associated correctly. There are a lot of pairends given, so perhaps lumpy can't handle that many. I'll start an issue in the lumpy repo with this and see if we can get any support over there https://github.com/arq5x/lumpy-sv/issues/383 .

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