search

Xinglab / espresso

Other
58 stars 4 forks source link

Out of memory #45

Open Jean497 opened 10 months ago

Jean497 commented 10 months ago

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 commented 10 months ago

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

EricKutschera commented 10 months ago

I think Out of memory! is from an old version of the Storable package: https://github.com/Xinglab/espresso/issues/30