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ryanlayer / giggle

Interval data structure
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Segmentation fault #52

Open kopardev opened 4 years ago

kopardev commented 4 years ago

Everything worked as expected until I had more than 1 million lines in my query file for "giggle search". Then it crashed with Segmentation Fault. After trying to do some quick debugging with gdb, I get the following backrace:

(gdb) backtrace
#0  0x0000000000408f30 in giggle_leaf_data_get_intersection_size ()
#1  0x0000000000408893 in giggle_collect_intersection_data_in_block ()
#2  0x000000000040882e in giggle_search ()
#3  0x000000000040a204 in giggle_query ()
#4  0x0000000000417eaa in search_main ()
#5  0x000000000040403a in main ()

Any help is appreciated. My original giggle command line was something like this:

giggle search -i mm10_tf_giggle_index -q tmp.1.5m.bed.gz
ryanlayer commented 4 years ago

Do you think you ran out of memory? Can you try recompiling so you get line numbers in gdb?

On Fri, May 15, 2020 at 4:33 PM Vishal Koparde notifications@github.com wrote:

Everything worked as expected until I had more than 1 million lines in my query file for "giggle search". Then it crashed with Segmentation Fault. After trying to do some quick debugging with gdb, I get the following backrace:

(gdb) backtrace

0 0x0000000000408f30 in giggle_leaf_data_get_intersection_size ()

1 0x0000000000408893 in giggle_collect_intersection_data_in_block ()

2 0x000000000040882e in giggle_search ()

3 0x000000000040a204 in giggle_query ()

4 0x0000000000417eaa in search_main ()

5 0x000000000040403a in main ()

Any help is appreciated. My original giggle command line was something like this:

giggle search -i mm10_tf_giggle_index -q tmp.1.5m.bed.gz

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