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Out of memory #45

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Jean497 opened this issue Jan 9, 2024 · 2 comments
Open

Out of memory #45

Jean497 opened this issue Jan 9, 2024 · 2 comments

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@Jean497
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Jean497 commented Jan 9, 2024

This is my Nanopore R10.4 data

"General summary:
Mean read length: 676.5
Mean read quality: 16.1
Median read length: 586.0
Median read quality: 16.9
Number of reads: 13,380,478.0
Read length N50: 695.0
STDEV read length: 320.7
Total bases: 9,052,322,967.0"

When i run ESPRESSO_S.pl, it's always
[Tue Jan 9 12:03:19 2024] Loading reference
Out of memory!
Perl exited with active threads:
1 running and unjoined
0 finished and unjoined
0 running and detached

But my available memory is
"top - 12:08:34 up 61 days, 15:59, 1 user, load average: 0.04, 0.17, 0.18
Tasks: 385 total, 1 running, 298 sleeping, 0 stopped, 0 zombie
%Cpu(s): 0.4 us, 0.7 sy, 0.0 ni, 98.8 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 65834484 total, 27439324 free, 4896112 used, 33499048 buff/cache
KiB Swap: 48827388 total, 47374536 free, 1452852 used. 60189184 avail Mem "

Even if I use a thread, it will still report an error. Do you know how to handle this error report?

@Jean497
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Jean497 commented Jan 9, 2024

I split my genome reference and sam file into single chromosome, it finally worked.

@EricKutschera
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I think Out of memory! is from an old version of the Storable package: #30

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