Description of bug
Hi,
I encountered a problem while running SPAdes. I've attached the log and param file below.
params.txt
spades.log
Environment:
SPAdes version: 4.0.0
Python version: 3.10.14
OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
I'm running SPAdes on an HPC cluster using the following command:
spades.py -1 READ_QC/N/final_pure_reads_1.fastq -2 READ_QC/N/final_pure_reads_2.fastq -m 1024 -t 32 --meta -o metaspades_N
Error:
== Error == system call for: "['/mgpfs/home/joko047/.conda/envs/wgs/bin/spades-hammer', '/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info']" finished abnormally, OS return value: -9
Could you help me understand what might be causing the issue?
Thank you.
spades.log
Command line: /mgpfs/home/joko047/.conda/envs/wgs/bin/spades.py -1 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq -2 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq -m 1024 -t 32 --meta -o /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
System information:
SPAdes version: 4.0.0
Python version: 3.10.14
OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
Output dir: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq']
right reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
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: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/tmp
Threads: 32
Memory limit (in Gb): 1024
======= SPAdes pipeline started. Log can be found here: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/spades.log
/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq: max reads length: 151
/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq: max reads length: 151
Reads length: 151
===== Before start started.
===== Read error correction started.
===== Read error correction started.
== Running: /mgpfs/home/joko047/.conda/envs/wgs/bin/spades-hammer /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info
0:00:00.000 1M / 48M INFO General (main.cpp : 76) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.019 1M / 48M INFO General (main.cpp : 77) Loading config from "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info"
0:00:00.034 1M / 48M INFO General (main.cpp : 79) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.043 1M / 48M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb
0:00:00.043 1M / 48M INFO General (main.cpp : 87) Trying to determine PHRED offset
0:00:00.048 1M / 48M INFO General (main.cpp : 93) Determined value is 33
0:00:00.048 1M / 48M INFO General (hammer_tools.cpp : 40) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.048 1M / 48M INFO General (main.cpp : 114) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.048 1M / 48M INFO K-mer Counting (kmer_data.cpp : 284) Estimating k-mer count
0:00:00.135 513M / 542M INFO K-mer Counting (kmer_data.cpp : 289) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq"
0:03:46.009 513M / 546M INFO K-mer Counting (kmer_data.cpp : 298) Processed 112734664 reads
0:03:46.009 513M / 546M INFO K-mer Counting (kmer_data.cpp : 289) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq"
0:07:30.271 513M / 547M INFO K-mer Counting (kmer_data.cpp : 298) Processed 225469328 reads
0:07:30.271 513M / 547M INFO K-mer Counting (kmer_data.cpp : 303) Total 225469328 reads processed
0:07:31.111 513M / 547M INFO K-mer Counting (kmer_data.cpp : 306) Estimated 22224198115 distinct kmers
0:07:31.111 1M / 547M INFO K-mer Counting (kmer_data.cpp : 310) Filtering singleton k-mers
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (86981476352 bytes, address: 0x1531066f0000, alignment: 67108864, commit: 1)
0:07:49.251 82G / 82G INFO K-mer Counting (kmer_data.cpp : 316) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq"
1:56:50.356 82G / 82G INFO K-mer Counting (kmer_data.cpp : 325) Processed 112734664 reads
1:56:50.356 82G / 82G INFO K-mer Counting (kmer_data.cpp : 316) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq"
3:44:24.786 82G / 82G INFO K-mer Counting (kmer_data.cpp : 325) Processed 225469328 reads
3:44:24.786 82G / 82G INFO K-mer Counting (kmer_data.cpp : 330) Total 225469328 reads processed
3:44:24.817 82G / 82G INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 16 files using 32 threads. This might take a while.
3:44:24.817 82G / 82G INFO General (file_limit.hpp : 43) Open file limit set to 1024
3:44:24.817 82G / 82G INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 9.82218 Gb
3:44:24.817 82G / 82G INFO General (kmer_splitter.hpp : 102) Using cell size of 4194304
3:44:24.980 100G / 100G INFO K-mer Splitting (kmer_data.cpp : 98) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq"
3:44:57.955 100G / 112G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 9563722 reads
3:45:30.324 100G / 112G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 18880515 reads
3:46:02.692 100G / 112G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 28231959 reads
3:46:36.323 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 37807904 reads
3:47:09.465 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 47263244 reads
3:47:42.336 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 56662752 reads
3:48:15.865 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 66467865 reads
3:48:49.434 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 76260078 reads
3:49:22.839 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 86158082 reads
3:49:56.476 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 95977771 reads
3:50:30.227 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 105835816 reads
3:50:54.319 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 112734664 reads
3:50:54.319 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 98) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq"
3:52:33.472 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 141174973 reads
3:57:22.910 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 113) Total 225469328 reads processed
3:57:22.960 82G / 113G INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.
4:00:28.041 82G / 223G INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8955612502 kmers in total.
4:00:30.354 69M / 223G INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices
4:07:28.289 6334M / 223G INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 8955612502 kmers, 6468330656 bytes occupied (5.77812 bits per kmer).
4:07:28.289 6334M / 223G 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 (71651295232 bytes, address: 0x1534982f0000, alignment: 67108864, commit: 1)
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (71651295232 bytes, address: 0x1523e9400000, alignment: 67108864, commit: 1)
4:10:46.843 140G / 223G INFO General (main.cpp : 149) Clustering Hamming graph.
5:05:29.640 140G / 223G INFO General (main.cpp : 156) Extracting clusters:
5:05:29.640 140G / 223G INFO General (concurrent_dsu.cpp : 19) Connecting to root
5:05:40.887 140G / 223G INFO General (concurrent_dsu.cpp : 35) Calculating counts
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (146033082368 bytes, address: 0x1501e7c00000, alignment: 67108864, commit: 1)
== Error == system call for: "['/mgpfs/home/joko047/.conda/envs/wgs/bin/spades-hammer', '/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info']" finished abnormally, OS return value: -9
None
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: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/spades.log
Thank you for using metaSPAdes! If you use it in your research, please cite:
Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
doi.org/10.1101/gr.213959.116
params.txt
Command line: /mgpfs/home/joko047/.conda/envs/wgs/bin/spades.py -1 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq -2 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq -m 1024 -t 32 --meta -o /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
System information:
SPAdes version: 4.0.0
Python version: 3.10.14
OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
Output dir: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq']
right reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
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: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/tmp
Threads: 32
Memory limit (in Gb): 1024
SPAdes version
4.0.0
Operating System
Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
Python Version
3.10.14
Method of SPAdes installation
Conda
No errors reported in spades.log
Description of bug
Hi,
I encountered a problem while running SPAdes. I've attached the log and param file below.
params.txt
spades.log
Environment:
SPAdes version: 4.0.0
Python version: 3.10.14
OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
I'm running SPAdes on an HPC cluster using the following command:
spades.py -1 READ_QC/N/final_pure_reads_1.fastq -2 READ_QC/N/final_pure_reads_2.fastq -m 1024 -t 32 --meta -o metaspades_N
Error:
== Error == system call for: "['/mgpfs/home/joko047/.conda/envs/wgs/bin/spades-hammer', '/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info']" finished abnormally, OS return value: -9
Could you help me understand what might be causing the issue?
Thank you.
spades.log
Command line: /mgpfs/home/joko047/.conda/envs/wgs/bin/spades.py -1 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq -2 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq -m 1024 -t 32 --meta -o /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
System information:
SPAdes version: 4.0.0
Python version: 3.10.14
OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
Output dir: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq']
right reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
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: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/tmp
Threads: 32
Memory limit (in Gb): 1024
======= SPAdes pipeline started. Log can be found here: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/spades.log
/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq: max reads length: 151
/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq: max reads length: 151
Reads length: 151
===== Before start started.
===== Read error correction started.
===== Read error correction started.
== Running: /mgpfs/home/joko047/.conda/envs/wgs/bin/spades-hammer /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info
0:00:00.000 1M / 48M INFO General (main.cpp : 76) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.019 1M / 48M INFO General (main.cpp : 77) Loading config from "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info"
0:00:00.034 1M / 48M INFO General (main.cpp : 79) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.043 1M / 48M INFO General (memory_limit.cpp : 55) Memory limit set to 1024 Gb
0:00:00.043 1M / 48M INFO General (main.cpp : 87) Trying to determine PHRED offset
0:00:00.048 1M / 48M INFO General (main.cpp : 93) Determined value is 33
0:00:00.048 1M / 48M INFO General (hammer_tools.cpp : 40) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.048 1M / 48M INFO General (main.cpp : 114) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.048 1M / 48M INFO K-mer Counting (kmer_data.cpp : 284) Estimating k-mer count
0:00:00.135 513M / 542M INFO K-mer Counting (kmer_data.cpp : 289) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq"
0:03:46.009 513M / 546M INFO K-mer Counting (kmer_data.cpp : 298) Processed 112734664 reads
0:03:46.009 513M / 546M INFO K-mer Counting (kmer_data.cpp : 289) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq"
0:07:30.271 513M / 547M INFO K-mer Counting (kmer_data.cpp : 298) Processed 225469328 reads
0:07:30.271 513M / 547M INFO K-mer Counting (kmer_data.cpp : 303) Total 225469328 reads processed
0:07:31.111 513M / 547M INFO K-mer Counting (kmer_data.cpp : 306) Estimated 22224198115 distinct kmers
0:07:31.111 1M / 547M INFO K-mer Counting (kmer_data.cpp : 310) Filtering singleton k-mers
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (86981476352 bytes, address: 0x1531066f0000, alignment: 67108864, commit: 1)
0:07:49.251 82G / 82G INFO K-mer Counting (kmer_data.cpp : 316) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq"
1:56:50.356 82G / 82G INFO K-mer Counting (kmer_data.cpp : 325) Processed 112734664 reads
1:56:50.356 82G / 82G INFO K-mer Counting (kmer_data.cpp : 316) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq"
3:44:24.786 82G / 82G INFO K-mer Counting (kmer_data.cpp : 325) Processed 225469328 reads
3:44:24.786 82G / 82G INFO K-mer Counting (kmer_data.cpp : 330) Total 225469328 reads processed
3:44:24.817 82G / 82G INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 16 files using 32 threads. This might take a while.
3:44:24.817 82G / 82G INFO General (file_limit.hpp : 43) Open file limit set to 1024
3:44:24.817 82G / 82G INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 9.82218 Gb
3:44:24.817 82G / 82G INFO General (kmer_splitter.hpp : 102) Using cell size of 4194304
3:44:24.980 100G / 100G INFO K-mer Splitting (kmer_data.cpp : 98) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq"
3:44:57.955 100G / 112G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 9563722 reads
3:45:30.324 100G / 112G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 18880515 reads
3:46:02.692 100G / 112G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 28231959 reads
3:46:36.323 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 37807904 reads
3:47:09.465 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 47263244 reads
3:47:42.336 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 56662752 reads
3:48:15.865 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 66467865 reads
3:48:49.434 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 76260078 reads
3:49:22.839 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 86158082 reads
3:49:56.476 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 95977771 reads
3:50:30.227 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 105835816 reads
3:50:54.319 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 112734664 reads
3:50:54.319 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 98) Processing "/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq"
3:52:33.472 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 141174973 reads
3:57:22.910 100G / 113G INFO K-mer Splitting (kmer_data.cpp : 113) Total 225469328 reads processed
3:57:22.960 82G / 113G INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting.
4:00:28.041 82G / 223G INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8955612502 kmers in total.
4:00:30.354 69M / 223G INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices
4:07:28.289 6334M / 223G INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 8955612502 kmers, 6468330656 bytes occupied (5.77812 bits per kmer).
4:07:28.289 6334M / 223G 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 (71651295232 bytes, address: 0x1534982f0000, alignment: 67108864, commit: 1)
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (71651295232 bytes, address: 0x1523e9400000, alignment: 67108864, commit: 1)
4:10:46.843 140G / 223G INFO General (main.cpp : 149) Clustering Hamming graph.
5:05:29.640 140G / 223G INFO General (main.cpp : 156) Extracting clusters:
5:05:29.640 140G / 223G INFO General (concurrent_dsu.cpp : 19) Connecting to root
5:05:40.887 140G / 223G INFO General (concurrent_dsu.cpp : 35) Calculating counts
mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (146033082368 bytes, address: 0x1501e7c00000, alignment: 67108864, commit: 1)
== Error == system call for: "['/mgpfs/home/joko047/.conda/envs/wgs/bin/spades-hammer', '/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/corrected/configs/config.info']" finished abnormally, OS return value: -9
None
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: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/spades.log
Thank you for using metaSPAdes! If you use it in your research, please cite:
Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
doi.org/10.1101/gr.213959.116
params.txt
Command line: /mgpfs/home/joko047/.conda/envs/wgs/bin/spades.py -1 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq -2 /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq -m 1024 -t 32 --meta -o /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
System information:
SPAdes version: 4.0.0
Python version: 3.10.14
OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
Output dir: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_1.fastq']
right reads: ['/mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/READ_QC/N/final_pure_reads_2.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
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: /mgpfs/home/joko047/sentarum-TNDS_shotgun_metagenome/metaspades_N/tmp
Threads: 32
Memory limit (in Gb): 1024
SPAdes version
4.0.0
Operating System
Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.28
Python Version
3.10.14
Method of SPAdes installation
Conda
No errors reported in spades.log