ablab
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation
Description of bug
If I ignore this warning "mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (16538140672 bytes, address: 0x7f31c5449000, alignment: 67108864, commit: 1)" "mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (16538140672 bytes, address: 0x7f2dea400000, alignment: 67108864, commit: 1)" and proceed with the results generated by it for further analysis, is that okay? thanks for your help very much.
spades.log
======= SPAdes pipeline started. Log can be found here: /home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/spades4/spades.log
/home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/1.nor.fq.gz: max reads length: 150 /home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/2.nor.fq.gz: max reads length: 150
Reads length: 150
Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (150) is equal to or greater than 150
===== Before start started.
===== Read error correction started.
===== Read error correction started.
== Running: /home/sd01/RWW1/rww/install/anaconda3/envs/spades4.0/bin/spades-hammer /home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/spades4/corrected/configs/config.info
0:00:00.000 1M / 9M INFO General (main.cpp : 76) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.002 1M / 9M INFO General (main.cpp : 77) Loading config from "/home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/spades4/corrected/configs/config.info" 0:00:00.002 1M / 9M INFO General (main.cpp : 79) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.003 1M / 9M INFO General (memory_limit.cpp : 55) Memory limit set to 250 Gb 0:00:00.003 1M / 9M INFO General (main.cpp : 87) Trying to determine PHRED offset 0:00:00.005 1M / 9M INFO General (main.cpp : 93) Determined value is 33 0:00:00.005 1M / 9M INFO General (hammer_tools.cpp : 40) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.005 1M / 9M INFO General (main.cpp : 114) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.005 1M / 9M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 16 files using 32 threads. This might take a while. 0:00:00.006 1M / 9M INFO General (file_limit.hpp : 43) Open file limit set to 1024 0:00:00.006 1M / 9M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 2.60417 Gb 0:00:00.006 1M / 9M INFO General (kmer_splitter.hpp : 102) Using cell size of 4194304 0:00:00.013 19G / 19G INFO K-mer Splitting (kmer_data.cpp : 98) Processing "/home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/1.nor.fq.gz" 0:00:44.175 19G / 30G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 7636984 reads 0:01:29.238 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 15457007 reads 0:02:13.103 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 23046290 reads 0:02:58.138 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 30821559 reads 0:03:41.824 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 38475082 reads 0:04:12.364 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 43761961 reads 0:04:12.367 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 98) Processing "/home/sd01/RWW1/rww/rawdata/GX5/fastp/normalization15X/2.nor.fq.gz" 0:04:56.643 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 51539163 reads 0:05:39.375 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 59012264 reads 0:06:23.214 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 66791118 reads 0:07:06.620 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 74421289 reads 0:07:50.553 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 82201049 reads 0:08:21.233 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 87523922 reads 0:08:21.238 19G / 31G INFO K-mer Splitting (kmer_data.cpp : 113) Total 87523922 reads processed 0:08:22.733 1M / 31G INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 0:08:55.654 1M / 92G INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 2066303430 kmers in total. 0:08:55.660 1M / 92G INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 0:10:21.244 1475M / 92G INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 2066303430 kmers, 1492428856 bytes occupied (5.77816 bits per kmer). 0:10:21.247 1475M / 92G INFO K-mer Counting (kmer_data.cpp : 355) Arranging kmers in hash map order mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (16538140672 bytes, address: 0x7f31c5449000, alignment: 67108864, commit: 1) mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (16538140672 bytes, address: 0x7f2dea400000, alignment: 67108864, commit: 1) 0:11:36.469 33G / 92G INFO General (main.cpp : 149) Clustering Hamming graph.
params.txt
(spades4.0) sd01@sd01:~/RWW1/rww/rawdata/GX5/fastp/normalization15X$ time spades.py -1 1.nor.fq.gz -2 2.nor.fq.gz -o spades4 -t 32
SPAdes version
4.0.0
Operating System
Linux-5.15.0-117-generic-x86_64-with-glibc2.35
Python Version
3.8.19
Method of SPAdes installation
conda
No errors reported in spades.log
- [X] Yes
