getting error while running spades.py error : finished abnormally, OS return value: -11

[rishidash12]

Description of bug

I am running the following command "spades.py --rna -s mouse1_mRNA.fastq -o mouse1_spades -m 50 --phred-offset 33" getting error like this == Error == system call for: "['/home/ccmr_server/metatranscriptomics/SPAdes-3.15.5-Linux/bin/spades-core', '/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/config.info', '/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/mda_mode.info', '/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/rna_mode.info']" finished abnormally, OS return value: -11

initially ram and phred-offset i kept default then i reduced ram to 100 then 50 still got the same error. Please kindly help me to solve this.

spades.log

Command line: /home/ccmr_server/metatranscriptomics/SPAdes-3.15.5-Linux/bin/spades.py --rna -s /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_mRNA.fastq -o /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades -m 50 --phred-offset 33

System information:
SPAdes version: 3.15.5
Python version: 3.10.12
OS: Linux-5.15.0-91-generic-x86_64-with-glibc2.35

Output dir: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades
Debug mode is turned OFF

Dataset parameters:
RNA-seq mode
Reads:
Library number: 1, library type: single
left reads: not specified
right reads: not specified
interlaced reads: not specified
single reads: ['/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_mRNA.fastq']
merged reads: not specified
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/tmp
Threads: 16
Memory limit (in Gb): 50

======= SPAdes pipeline started. Log can be found here: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/spades.log

/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_mRNA.fastq: max reads length: 160

Reads length: 160

K values to be used: [53, 79]

===== Before start started.

===== Assembling started.

===== K53 started.

== Running: /home/ccmr_server/metatranscriptomics/SPAdes-3.15.5-Linux/bin/spades-core /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/config.info /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/mda_mode.info /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/rna_mode.info

0:00:00.000 1M / 17M INFO General (main.cpp : 99) Loaded config from /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/config.info
0:00:00.000 1M / 17M INFO General (main.cpp : 99) Loaded config from /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/mda_mode.info
0:00:00.000 1M / 17M INFO General (main.cpp : 99) Loaded config from /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/rna_mode.info
0:00:00.000 1M / 17M INFO General (memory_limit.cpp : 54) Memory limit set to 50 Gb
0:00:00.000 1M / 17M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.5, git revision e757b82
0:00:00.000 1M / 17M INFO General (main.cpp : 108) Maximum k-mer length: 128
0:00:00.000 1M / 17M INFO General (main.cpp : 109) Assembling dataset (/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/dataset.info) with K=53
0:00:00.000 1M / 17M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.000 1M / 17M INFO General (pipeline.cpp : 212) SPAdes started
0:00:00.000 1M / 17M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion
0:00:00.000 1M / 17M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled
0:00:00.000 1M / 17M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3
0:00:00.000 1M / 17M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40
0:00:00.001 1M / 17M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8
0:00:00.001 1M / 17M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion)
0:00:00.001 1M / 17M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)
0:00:00.001 1M / 17M INFO General (read_converter.cpp : 73) Converting paired reads
0:00:00.001 8M / 17M INFO General (binary_converter.cpp : 111) 0 reads written
0:00:00.001 1M / 17M INFO General (read_converter.cpp : 86) Converting single reads
0:00:00.129 11M / 24M INFO General (binary_converter.cpp : 96) 16384 reads processed
0:00:00.134 11M / 24M INFO General (binary_converter.cpp : 96) 32768 reads processed
0:00:00.145 11M / 25M INFO General (binary_converter.cpp : 96) 65536 reads processed
0:00:00.304 11M / 26M INFO General (binary_converter.cpp : 111) 82925 reads written
0:00:00.304 7M / 26M INFO General (read_converter.cpp : 92) Converting merged reads
0:00:00.305 11M / 26M INFO General (binary_converter.cpp : 111) 0 reads written
0:00:00.307 1M / 26M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction)
0:00:00.310 1M / 26M INFO General (construction.cpp : 153) Max read length 160
0:00:00.310 1M / 26M INFO General (construction.cpp : 159) Average read length 137.482
0:00:00.310 1M / 26M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
0:00:00.310 1M / 26M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 160 files using 16 threads. This might take a while.

== Error == system call for: "['/home/ccmr_server/metatranscriptomics/SPAdes-3.15.5-Linux/bin/spades-core', '/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/config.info', '/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/mda_mode.info', '/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/K53/configs/rna_mode.info']" finished abnormally, OS return value: -11

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or 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: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/spades.log

Thank you for using SPAdes!

params.txt

Command line: /home/ccmr_server/metatranscriptomics/SPAdes-3.15.5-Linux/bin/spades.py --rna -s /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_mRNA.fastq -o /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades -m 50 --phred-offset 33

System information:
SPAdes version: 3.15.5
Python version: 3.10.12
OS: Linux-5.15.0-91-generic-x86_64-with-glibc2.35

Output dir: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades
Debug mode is turned OFF

Dataset parameters:
RNA-seq mode
Reads:
Library number: 1, library type: single
left reads: not specified
right reads: not specified
interlaced reads: not specified
single reads: ['/home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_mRNA.fastq']
merged reads: not specified
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades/tmp
Threads: 16
Memory limit (in Gb): 50

SPAdes version

SPAdes v3.15.5

Operating System

Linux-5.15.0-91-generic-x86_64-with-glibc2.35

Python Version

Python v3.10.12

Method of SPAdes installation

binaries

No errors reported in spades.log

• Yes

[asl]

You might hit limit of # of opened files. Likely more information could be found in the system log.

[rishidash12]

I find system log files don't know which one to see for the spades errors.

[kovcsboti]

I got the same error message when I ran spades 3.15.4 on bacterial genome, however it ran fine with spades 3.13.1 and it ran without problem (not sure if it helps, just letting you know).

[rishidash12]

@kovcsboti
I tried using 3.13.1 version of SPAdes but now its showing a different error. Not hashable.
/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/bin/spades.py:13: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils import dir_util
Command line: /home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/bin/spades.py --rna -s /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_mRNA.fastq -o /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades

System information:
SPAdes version: 3.13.1
Python version: 3.10.12
OS: Linux-5.15.0-91-generic-x86_64-with-glibc2.35

Output dir: /home/ccmr_server/metatranscriptomics/new_workshop_file/mouse1_spades
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
RNA-seq mode
Reads:
Traceback (most recent call last):
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/bin/spades.py", line 1102, in
main(sys.argv)
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/bin/spades.py", line 721, in main
print_used_values(cfg, log)
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/bin/spades.py", line 110, in print_used_values
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/share/spades/pyyaml3/init.py", line 72, in load
return loader.get_single_data()
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/share/spades/pyyaml3/constructor.py", line 37, in get_single_data
return self.construct_document(node)
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/share/spades/pyyaml3/constructor.py", line 46, in construct_document
for dummy in generator:
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/share/spades/pyyaml3/constructor.py", line 398, in construct_yaml_map
value = self.construct_mapping(node)
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/share/spades/pyyaml3/constructor.py", line 204, in construct_mapping
return super().construct_mapping(node, deep=deep)
File "/home/ccmr_server/metatranscriptomics/new_workshop_file/SPAdes-3.13.1-Linux/share/spades/pyyaml3/constructor.py", line 126, in construct_mapping
if not isinstance(key, collections.Hashable):
AttributeError: module 'collections' has no attribute 'Hashable'

[asl]

AttributeError: module 'collections' has no attribute 'Hashable'

This is a known issue fixed in 3.15.3. 3.13.1 is simply ancient and contains known issues

[rishidash12]

But Sir @asl I am also facing issues in 3.15.5 version of Spades and i.e. finished abnormally, OS return value: -11. Please help me to resolve this problem.