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GuipengLi / ChIA-PET2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data
GNU General Public License v3.0
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bedpe2Interaction core dumped #30

Closed hugch2020 closed 2 years ago

hugch2020 commented 2 years ago

Hi @GuipengLi , An error was reported when I run bedpe2Interaction.

bedpe2Interaction RAD21_ChIAPET.rmdup.bedpe.tmp RAD21_ChIAPET.interactions RAD21_ChIAPET.stat Running bedpe2Interaction... Segmentation fault (core dumped)

The input file format is as follows, head RAD21_ChIAPET.rmdup.bedpe.tmp chrX 38634826 38634927 chrX 38634869 38634970 SRR8659342.732269 . + - chrX 38633862 38635745 553 chrX 38634826 38634927 chrX 38634869 38634970 SRR8659342.732269 . + - chrX 38633862 38635745 553 chrX 36866684 36866785 chrX 36866967 36867066 SRR8659342.4394649 . + - chrX 36866138 36868189 237 chrX 36866684 36866785 chrX 36866967 36867066 SRR8659342.4394649 . + - chrX 36866138 36868189 237 chr15 77107681 77107782 chr15 77107755 77107797 SRR8659342.2501571 . + - chr15 77106748 77108892 996 chr15 77107681 77107782 chr15 77107755 77107797 SRR8659342.2501571 . + - chr15 77106748 77108892 996 chrX 37059730 37059831 chrX 37059852 37059953 SRR8659342.3183715 . + - chrX 37059546 37061952 380 chrX 37059730 37059831 chrX 37059852 37059953 SRR8659342.3183715 . + - chrX 37059546 37061952 380 chr15 74373832 74373933 chr15 74373935 74374036 SRR8659342.8464568 . + - chr15 74372747 74376257 3104 chr15 74373832 74373933 chr15 74373935 74374036 SRR8659342.8464568 . + - chr15 74372747 74376257 3104

I have no idea where the problem is, could you give me some advice. Thanks so much!

GuipengLi commented 2 years ago

How did you generated this file RAD21_ChIAPET.rmdup.bedpe.tmp ? bedpe2Interaction is used internally within ChIA-PET2. The input file format should be correct.

hugch2020 commented 2 years ago

You're right. I found that I didn't add peak name after bedSlop, so the format of bedpe.tmp is not correct. Thanks!