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Command terminated by signal 11 when decompress (memory error) #1

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ttan6729 opened this issue Jul 5, 2021 · 0 comments
Open

Command terminated by signal 11 when decompress (memory error) #1

ttan6729 opened this issue Jul 5, 2021 · 0 comments

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@ttan6729
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ttan6729 commented Jul 5, 2021

bug_set.zip

Hi, thanks for this awesome two-level compression tool and other libraries for genome and reads compression.
Currently I am testing the performance of state-of-the-art compression algorithms on datasets with a large number of small genomes. GDC2 shows great performance in compression, but return signal 11 (memory error) during decompression of some datasets. One example is shown in the attached file (include 175 genomes and two lists, 173.txt and 174.txt). In my cluster, gdc2 compress and decompress 173.txt (include 174 genomes, the first one is reference) correctly, but return error when decompressing 174.txt. GDC2 is able to decompress OD996576.1.fa separeately, which is the only difference between 173.txt and 174.txt. In addition, GDC2 also works fine on a set of 132372 genomes. Hence I can't find the cause of this error based on the difference in sequence number or other factor.

OD996576.1.fa

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