Bedtools intersect truncates bed12 intervals

[ddubocan]

Hi,

I am working with the bed12 file format. When I perform bedtools intersect with the -wa flag, my intervals get truncated in the output file. Typically the truncation occurs in the 12th field, leading me to believe its some issue with handling longer lines.

Thanks in advance for the help,
Danilo

[arq5x]

Which version are you using and can you provide an example command and dataset that produces the problem?

[ddubocan]

bedtools v2.30.0

bedtools intersect -wa -a example_bed12.bed -b region.bed

example_bed12.bed:

chr1 46626685 46645317 1527 4.01 . 46626685 46645317 128,0,128 102 1,104,89,167,139,135,140,141,107,94,153,178,132,162,163,147,131,133,187,146,201,242,98,156,171,167,163,153,143,143,156,143,155,119,142,139,157,94,201,163,163,160,157,154,129,147,163,158,151,170,133,144,146,151,168,132,319,205,149,132,161,153,146,140,166,130,153,151,100,179,158,156,189,178,141,130,136,168,146,176,157,124,131,166,175,152,201,184,111,123,212,148,169,340,166,260,141,154,156,139,159,1 0,99,223,403,601,794,938,1124,1324,1527,1633,1787,2021,2176,2347,2522,2752,2931,3079,3276,3434,3636,3879,3987,4146,4352,4550,4740,4915,5069,5235,5441,5600,5780,5919,6097,6264,6490,6599,6805,6969,7177,7384,7559,7766,7929,8077,8275,8469,8640,8859,9012,9163,9341,9544,9713,9902,10222,10447,10600,10788,10969,11149,11314,11479,11699,11882,12065,12297,12431,12625,12793,12955,13145,13344,13517,13681,13822,14018,14205,14382,14580,14733,14910,15094,15272,15462,15667,15852,16022,16173,16406,16593,16827,17168,17335,17690,17834,18082,18264,18442,18631

region.bed:

chr1 43250001 47250000

The output looks like:

chr1 46626685 46645317 1527 4.01 . 46626685 46645317 128,0,128 102 1,104,89,167,139,135,140,141,107,94,153,178,132,162,163,147,131,133,187,146,201,242,98,156,171,167,163,153,143,143,156,143,155,119,142,139,157,94,201,163,163,160,157,154,129,147,163,158,151,170,133,144,146,151,168,132,319,205,149,132,161,153,146,140,166,130,153,151,100,179,158,156,189,178,141,130,136,168,146,176,157,124,131,166,175,152,201,184,111,123,212,148,169,340,166,260,141,154,156,139,159,1 0,99,223,403,601,794,938,1124,1324,1527,1633,1787,2021,2176,2347,2522,2752,2931,3079,3276,3434,3636,3879,3987,4146,4352,4550,4740,4915,5069,5235,5441,5600,5780,5919,6097,6264,6490,6599,6805,6969,7177,7384,7559,7766,7929,8077,8275,8469,8640,8859,9012,9163,9341,9544,9713,9902,10222,10447,10600,10788,10969,11149,11314,11479,11699,11882,12065,12297,12431,12625,12793,12955,13145,13344,13517,13681,13822,14018,14205,14382,14580,14733,14910,15094,15272,15462,15667,15852,16022,16173,16406,16593,16827,17168,17335,17690,17834,18082,182

You can see that the last 3 values from the 12th field are missing/cutoff.
Thanks

[arq5x]

Thanks. I am unable to reproduce this on my laptop. Is it possible that your terminal is truncating the output? You could test this by writing the output to a file and checking the contents

[ddubocan]

That interval is pulled directly from a file. I've been redirecting stdout to a file.

It very well may be the system I am using, I will try the same command on a different system and see if that fixes this issue.

Thanks again for your prompt help!

[vinzenzmay]

Hi, I have the exact same problem, both on Ubuntu 20.04, bash 5.1.16(1), bedtools v2.30.0; and Rocky Linux 8.5, bash 4.4.20(1), bedtools v2.30.0.
@ddubocan have you found a solution?

[cwhelan]

I've also experienced similar behavior, with bedtools v2.30.0 on Ubuntu 22.04/bash 5.1.16(1). In my case I had encoded a long string in the fourth (name) column of the bed interval and that field was truncated after 1004 characters. If there's additional information I can provide that would be helpful let me know.

[arq5x]

@brentp could you test this with the version in main? I am fairly certain this is fixed, motivating the urgency for me to make a new formal release