search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
752 stars 135 forks source link

======= SPAdes pipeline finished abnormally and WITH WARNINGS! #1190

Open scleractinia opened 1 year ago

scleractinia commented 1 year ago

Description of bug

I can't seem to figure out what the problem is. I am not sure what I should do about the no-saved checkpoints. The warning message reads as follows.

warning.log (below)

=== Error correction and assembling warnings:

spades.log

3:33:49.984 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 104000000 edges 3:40:56.225 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 112000000 edges 3:47:58.791 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 120000000 edges 3:55:24.302 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 128000000 edges 4:02:56.134 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 136000000 edges 4:10:25.294 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 144000000 edges 6:16:45.435 56G / 56G INFO General (coverage_filling.hpp : 82) Processed 272000000 edges 7:13:09.396 32G / 32G INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 7:13:09.565 32G / 32G INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 7:22:08.308 34G / 34G INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 82317998 out of 324997012, length: 18446744073191093805 7:22:19.417 35G / 35G INFO General (edge_index.hpp : 167) Using small index (max_id = 326625109) 7:23:04.092 35G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 7:29:48.828 37G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 2831081292 kmers, 2044789568 bytes occupied (5.77812 bits per kmer). 7:30:06.932 58G / 58G INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while.

== Error == system call for: "['/Users/carolinacarpenter/miniconda3/envs/assembly/bin/spades-core', '/Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20/K55/configs/config.info', '/Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20/K55/configs/mda_mode.info', '/Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20/K55/configs/meta_mode.info']" finished abnormally, OS return value: -9

======= SPAdes pipeline finished abnormally and WITH WARNINGS!

=== Error correction and assembling warnings:

=== ERRORs:

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: /Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20/spades.log

Thank you for using SPAdes!

params.txt

Command line: /Users/carolinacarpenter/miniconda3/envs/assembly/bin/spades.py -1 /Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/G_ZymoPCR20_S9_L003_R1_001.fastq.gz -2 /Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/G_ZymoPCR20_S9_L003_R2_001.fastq.gz --meta --only-assembler -o /Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20

System information: SPAdes version: 3.15.2 Python version: 3.11.5 OS: macOS-14.0-x86_64-i386-64bit

Output dir: /Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20 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: ['/Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/G_ZymoPCR20_S9_L003_R1_001.fastq.gz'] right reads: ['/Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/G_ZymoPCR20_S9_L003_R2_001.fastq.gz'] interlaced reads: not specified 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 Other parameters: Dir for temp files: /Users/carolinacarpenter/Documents/1.projects/coral-awol/data/round1/metagenomics/02_fastp_QC/ZymoPCR20/tmp Threads: 16 Memory limit (in Gb): 250

SPAdes version

3.15.2

Operating System

macOS Sonoma 14.0

Python Version

3.11.5

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 1 year ago

Hello

Will you please attach the proper complete spades.log file?

scleractinia commented 1 year ago

spades.log

asl commented 1 year ago

Your SPAdes job was killed. Likely you can find more information in the system log, but I'd suspect you're running out of RAM