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ESPRESSO_S out of memory！ #30

Closed kir1to455 closed 1 year ago

kir1to455 commented 1 year ago

Hi, Thank you for developing ESPRESSO! I encountered the following issues while running ESPRESSO_S.pl. My ESPRESSO version is 1.3.2. Here is my code. perl ${ESPRESSO_Dir}/ESPRESSO_S.pl -A ${IndexDir}/gencode.vM33.basic.annotation.gtf -L ${HomeDir}/samples.tsv -F ${IndexDir}/GRCm39.genome.fa -O ${Output_Dir} -T 10 image I am sure it is not caused by memory, as my machine has 256GB of memory and it automatically terminates when it occupies 2.2GB of memory.

Could you give me some advice? Best wishes, Kirito

kir1to455 commented 1 year ago

I successfully ran ESPRESSO_S.pl in ESPRESSO1.3.0 version.

bingqiWu commented 10 months ago

I met the same problem, too. still not figure out how to solve it.

EricKutschera commented 10 months ago

I think the Out of memory! message comes from the Storable package. ESPRESSO needs Storable version >= 3: https://github.com/Xinglab/espresso/tree/v1.4.0#dependencies https://perldoc.perl.org/Storable#huge-objects

You can check the version with: perl -e 'use Storable; print("$Storable::VERSION\n")'