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
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 e757b8216f9a038fb616e9551a2d4891b2d19ad7
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
/home/ccmr_server/metatranscriptomics/SPAdes-3.15.5-Linux/bin/spades.py --rna -s mouse1_mRNA.fastq -o mouse1_spades -m 50 --phred-offset 33
== Warning == output dir is not empty! Please, clean output directory before run.
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 e757b8216f9a038fb616e9551a2d4891b2d19ad7 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!