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WGLab / LinkedSV

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no "images" directory #27

Open MartaRusmini opened 2 years ago

MartaRusmini commented 2 years ago

Hi I'm running linkedSV on two of linked-read WGS. One has a tandem duplication, the other a known translocation. This is my command: linkedsv.py -i sample.phased_possorted_bam.bam -d path -r path/genome.fa -v hg38 -t 20 --wgs --germline_mode

It seems to work well (no error) and I obtained the following files: image

but I cannot see the "images" directory. Can you help me? Moreover, I cannot find in the bedpe or other files, neither the duplication (is a 13Kb dup) nor the translocation. Do you know why?

thnk you

fangli80 commented 2 years ago

Hello, Could you please share me the stdout and stderr of LinkedSV? Thanks, Li

MartaRusmini commented 2 years ago

Here the files in attachment

thank you T514.linSV.err.txt https://drive.google.com/file/d/1wu4MhXeBIvmFpqo4UlcMssgYEin_zENX/view?usp=drive_web T514.linSV.out.txt https://drive.google.com/file/d/14xHiKYaJHsf8dm3C6Pwob69nLAmtczso/view?usp=drive_web

Il giorno mar 1 feb 2022 alle ore 09:33 Li Fang @.***> ha scritto:

Hello, Could you please share me the stdout and stderr of LinkedSV? Thanks, Li

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MartaRusmini commented 2 years ago

sorry, Can you please help me with this issue?