os return value:-11

[Wanli-HE]

Description of bug

hi there,

i am trying to assembly some samples, i got some issues, like

== Error == system call for: "['/cfs/klemming/projects/supr/uppstore2017096/users/wanlihe/tools/Plaspline/conda_envs/7fb4b10ca90d24e6107c25c2bda9c5b9_/bin/spades-core', '/cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/config.info', '/cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/mda_mode.info', '/cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/meta_mode.info']" finished abnormally, OS return value: -11

command line "/cfs/klemming/projects/supr/uppstore2017096/users/wanlihe/tools/Plaspline/conda_envs/7fb4b10ca90d24e6107c25c2bda9c5b9_/bin/spades.py --only-assembler --12 /cfs/klemming/scratch/w/wanlihe/Elbere_2020_reads/ERR7132564_matched.fastq.gz --meta -m 5000 -t 30 -k 21,33,55 -o /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res"

version is 4.1.0

python is 3.13.2

do you have any suggestions in this?

best,
wanli

spades.log

Command line: /cfs/klemming/projects/supr/uppstore2017096/users/wanlihe/tools/Plaspline/conda_envs/7fb4b10ca90d24e6107c25c2bda9c5b9_/bin/spades.py --only-assembler --12 /cfs/klemming/scratch/w/wanlihe/Elbere_2020_reads/ERR7132564_matched.fastq.gz --meta -m 5000 -t 30 -k 21,33,55 -o /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res

System information:
SPAdes version: 4.1.0
Python version: 3.13.2
OS: Linux-5.14.21-150500.55.65_13.0.73-cray_shasta_c-x86_64-with-glibc2.31

Output dir: /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/cfs/klemming/scratch/w/wanlihe/Elbere_2020_reads/ERR7132564_matched.fastq.gz']
single reads: not specified
merged reads: not specified
Assembly parameters:
k: [21, 33, 55]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Assembly graph output will use GFA v1.2 format
Other parameters:
Dir for temp files: /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/tmp
Threads: 30
Memory limit (in Gb): 5000

======= SPAdes pipeline started. Log can be found here: /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/spades.log

/cfs/klemming/scratch/w/wanlihe/Elbere_2020_reads/ERR7132564_matched.fastq.gz: max reads length: 333

Reads length: 333

===== Before start started.

===== Preprocess reads started.

===== Preprocess reads finished.

===== Assembling started.

===== K21 started.

== Running: /cfs/klemming/projects/supr/uppstore2017096/users/wanlihe/tools/Plaspline/conda_envs/7fb4b10ca90d24e6107c25c2bda9c5b9_/bin/spades-core /cfs/klemming/scra
tch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/config.info /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs
/mda_mode.info /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/meta_mode.info

0:00:00.000 1M / 26M INFO General (main.cpp : 94) Loaded config from "/cfs/klemming/scratch/w/wanlihe/assembly_res_Elb
ere/ERR7132564_spades_res/K21/configs/config.info"
0:00:00.004 1M / 26M INFO General (main.cpp : 94) Loaded config from "/cfs/klemming/scratch/w/wanlihe/assembly_res_Elb
ere/ERR7132564_spades_res/K21/configs/mda_mode.info"
0:00:00.004 1M / 26M INFO General (main.cpp : 94) Loaded config from "/cfs/klemming/scratch/w/wanlihe/assembly_res_Elb
ere/ERR7132564_spades_res/K21/configs/meta_mode.info"
0:00:00.004 1M / 26M INFO General (memory_limit.cpp : 55) Memory limit set to 5000 Gb
0:00:00.004 1M / 26M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A
0:00:00.004 1M / 26M INFO General (main.cpp : 103) Maximum k-mer length: 128
0:00:00.004 1M / 26M INFO General (main.cpp : 104) Assembling dataset ("/cfs/klemming/scratch/w/wanlihe/assembly_res_El
bere/ERR7132564_spades_res/dataset.info") with K=21
0:00:00.004 1M / 26M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 30
0:00:00.004 1M / 26M INFO General (pipeline.cpp : 212) SPAdes started
0:00:00.005 1M / 26M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion
0:00:00.005 1M / 26M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled
0:00:00.005 1M / 26M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3
0:00:00.005 1M / 26M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40
0:00:00.005 1M / 26M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8
0:00:00.005 1M / 26M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion)
0:00:00.009 1M / 26M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while)
0:00:00.009 1M / 26M INFO General (read_converter.cpp : 99) Converting paired reads
0:00:00.413 55M / 74M INFO General (binary_converter.cpp : 127) 16384 reads processed
0:00:00.421 55M / 74M INFO General (binary_converter.cpp : 127) 32768 reads processed
0:00:00.608 55M / 104M INFO General (binary_converter.cpp : 127) 65536 reads processed
0:00:00.608 55M / 104M INFO General (binary_converter.cpp : 127) 65536 reads processed
0:00:00.801 55M / 122M INFO General (binary_converter.cpp : 127) 131072 reads processed
0:00:01.398 6M / 160M INFO General (binary_converter.cpp : 127) 262144 reads processed
0:00:02.577 0M / 253M INFO General (binary_converter.cpp : 127) 524288 reads processed
0:00:04.789 0M / 389M INFO General (binary_converter.cpp : 127) 1048576 reads processed
0:00:09.317 0M / 609M INFO General (binary_converter.cpp : 127) 2097152 reads processed
0:00:12.508 0M / 627M INFO General (binary_converter.cpp : 143) 2798872 reads written
0:00:12.527 0M / 627M INFO General (read_converter.cpp : 113) Converting single reads
0:00:12.533 0M / 627M INFO General (binary_converter.cpp : 143) 0 reads written
0:00:12.533 0M / 627M INFO General (read_converter.cpp : 119) Converting merged reads
0:00:12.557 0M / 627M INFO General (binary_converter.cpp : 143) 0 reads written
0:00:12.564 1M / 627M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction)
0:00:12.637 1M / 627M INFO General (construction.cpp : 150) Max read length 362
0:00:12.638 1M / 627M INFO General (construction.cpp : 156) Average read length 167.823
0:00:12.639 1M / 627M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
0:00:12.639 1M / 627M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 300 files using 30 threads. This might
take a while.
0:00:12.640 2M / 627M INFO General (file_limit.hpp : 43) Open file limit set to 16384
0:00:12.640 2M / 627M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 55.5555 Gb
0:00:12.641 2M / 627M INFO General (kmer_splitter.hpp : 102) Using cell size of 223696
0:00:20.247 18G / 19G INFO General (kmer_splitters.hpp : 128) Processed 11195488 reads
0:00:20.251 2M / 19G INFO General (kmer_splitters.hpp : 134) Used 11195488 reads
0:00:20.269 2M / 19G INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.
0:00:21.054 2M / 19G INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 294431323 kmers in total.
0:00:21.054 2M / 19G INFO General (stage.cpp : 121) PROCEDURE == Extension index construction (id: construction:extensio
n_index_construction)
0:00:21.114 2M / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index
0:00:21.114 2M / 19G INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 300 files using 30 threads. This might
take a while.
0:00:21.115 3M / 19G INFO General (file_limit.hpp : 43) Open file limit set to 16384
0:00:21.115 3M / 19G INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 55.5555 Gb
0:00:21.115 3M / 19G INFO General (kmer_splitter.hpp : 102) Using cell size of 223696
0:00:23.737 18G / 19G INFO General (kmer_splitters.hpp : 197) Processed 8126447 kmers
0:00:24.858 18G / 19G INFO General (kmer_splitters.hpp : 197) Processed 37416560 kmers
0:00:25.928 18G / 19G INFO General (kmer_splitters.hpp : 197) Processed 66929306 kmers
0:00:27.043 18G / 19G INFO General (kmer_splitters.hpp : 197) Processed 96411245 kmers
0:00:28.459 18G / 19G INFO General (kmer_splitters.hpp : 197) Processed 125897940 kmers
0:00:29.803 18G / 19G INFO General (kmer_splitters.hpp : 197) Processed 155346687 kmers
0:00:31.153 18G / 20G INFO General (kmer_splitters.hpp : 197) Processed 184777161 kmers
0:00:32.526 18G / 20G INFO General (kmer_splitters.hpp : 197) Processed 214174336 kmers
0:00:33.814 18G / 20G INFO General (kmer_splitters.hpp : 197) Processed 243578306 kmers
0:00:35.141 18G / 20G INFO General (kmer_splitters.hpp : 197) Processed 272969665 kmers
0:00:36.260 18G / 20G INFO General (kmer_splitters.hpp : 197) Processed 294432973 kmers
0:00:36.260 18G / 20G INFO General (kmer_splitters.hpp : 197) Processed 294432973 kmers
0:00:36.261 18G / 20G INFO General (kmer_splitters.hpp : 202) Used 294432973 kmers.
0:00:36.264 3M / 20G INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.
0:00:37.827 3M / 20G INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 291455929 kmers in total.
0:00:37.828 3M / 20G INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices
0:00:40.987 209M / 20G INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 291455929 kmers, 210735120 bytes occupied (5.7843
4 bits per kmer).
0:00:40.987 209M / 20G INFO General (kmer_index_builder.hpp : 168) Merging final buckets.
0:00:46.373 489M / 20G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers
0:00:58.108 489M / 20G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished.
0:00:58.465 488M / 20G INFO General (stage.cpp : 121) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
0:00:58.465 488M / 20G INFO General (construction.cpp : 298) Early tip clipper length bound set as (RL - K)
0:00:58.465 488M / 20G INFO Early tip clipping (early_simplification.hpp : 48) Early tip clipping
0:01:07.030 638M / 20G INFO Early tip clipping (early_simplification.hpp : 83) #tipped junctions: 1313032
0:01:07.093 638M / 20G INFO Early tip clipping (early_simplification.hpp : 94) Clipped tips: 1315798
0:01:07.253 488M / 20G INFO Early tip clipping (early_simplification.hpp : 50) 31225869 22-mers were removed by early tip clipper
0:01:07.253 488M / 20G INFO General (stage.cpp : 121) PROCEDURE == Condensing graph (id: construction:graph_condensing)
0:01:07.262 489M / 20G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths
0:01:20.244 933M / 20G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 10628107 sequences extracted
0:01:26.859 933M / 20G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops
0:01:27.906 934M / 20G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 152 loops collected
0:01:28.230 933M / 20G INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges...
0:01:28.453 933M / 20G INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted
0:01:28.453 933M / 20G INFO General (debruijn_graph_constructor: 516) Total 21256518 edges to create
0:01:28.453 1752M / 20G INFO General (debruijn_graph_constructor: 519) Collecting link records
0:01:39.632 2080M / 20G INFO General (debruijn_graph_constructor: 521) Ordering link records
0:01:39.780 2080M / 20G INFO General (debruijn_graph_constructor: 524) Sorting done
0:01:39.847 2144M / 20G INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords...
0:01:40.011 2144M / 20G INFO General (debruijn_graph_constructor: 540) LinkRecords sorted
0:01:40.011 2144M / 20G INFO General (debruijn_graph_constructor: 542) Total 7652865 vertices to create
0:01:40.012 2853M / 20G INFO General (debruijn_graph_constructor: 545) Connecting the graph
0:01:49.616 2298M / 20G INFO General (stage.cpp : 121) PROCEDURE == Filling coverage indices (PHM) (id: construction:covera
ge_filling_phm)
0:01:49.617 2298M / 20G INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices
0:01:52.650 2505M / 20G INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 294431323 kmers, 212881984 bytes occupied (5.7842
2 bits per kmer).
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (1182793728 bytes, address: 0x7f30f6582000, alignment: 67108864, commi
t: 1)
0:01:52.793 3629M / 20G INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while
.
0:02:10.917 3629M / 20G INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM
0:02:23.501 3629M / 20G INFO General (coverage_filling.hpp : 83) Processed 21255741 edges
0:02:25.536 1810M / 20G INFO StageManager (stage.cpp : 189) STAGE == Raw Simplification (id: raw_simplification)
0:02:25.537 1810M / 20G INFO General (simplification.cpp : 129) PROCEDURE == Initial cleaning
0:02:25.537 1810M / 20G INFO Simplification (parallel_processing.hpp : 168) Running Self conjugate edge remover
0:02:25.704 1810M / 20G INFO Simplification (parallel_processing.hpp : 171) Self conjugate edge remover triggered 0 times
0:02:25.704 1810M / 20G INFO Simplification (parallel_processing.hpp : 168) Running Initial tip clipper
0:02:26.237 1811M / 20G INFO Simplification (parallel_processing.hpp : 171) Initial tip clipper triggered 31718 times
0:02:26.238 1811M / 20G INFO Simplification (parallel_processing.hpp : 168) Running Initial ec remover

== Error == system call for: "['/cfs/klemming/projects/supr/uppstore2017096/users/wanlihe/tools/Plaspline/conda_envs/7fb4b10ca90d24e6107c25c2bda9c5b9_/bin/spades-co
re', '/cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/config.info', '/cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR713
2564_spades_res/K21/configs/mda_mode.info', '/cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/K21/configs/meta_mode.info']" finished abnorma
lly, OS return value: -11

In case you have troubles running SPAdes, you can report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

SPAdes log can be found here: /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res/spades.log

params.txt

/cfs/klemming/projects/supr/uppstore2017096/users/wanlihe/tools/Plaspline/conda_envs/7fb4b10ca90d24e6107c25c2bda9c5b9_/bin/spades.py --only-assembler --12 /cfs/klemming/scratch/w/wanlihe/Elbere_2020_reads/ERR7132564_matched.fastq.gz --meta -m 5000 -t 30 -k 21,33,55 -o /cfs/klemming/scratch/w/wanlihe/assembly_res_Elbere/ERR7132564_spades_res"

SPAdes version

4.1.0

Operating System

linux

Python Version

3.13.2

Method of SPAdes installation

conda

No errors reported in spades.log

• Yes