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SPAdes Genome Assembler
http://ablab.github.io/spades/
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Error == system call for Spades spades-core #1136

Closed emmannaemeka closed 1 year ago

emmannaemeka commented 1 year ago

Description of bug

Hello, I am having troubles running Spades. It kept throwing up this error

ibrary number: 1, library type: paired-end orientation: fr left reads: ['/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq', '/Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq'] right reads: ['/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq', '/Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq'] interlaced reads: not specified single reads: not specified 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: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/tmp Threads: 16 Memory limit (in Gb): 250

======= SPAdes pipeline started. Log can be found here: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/spades.log

/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq: max reads length: 151 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq: max reads length: 151 /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq: max reads length: 151 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq: max reads length: 151

Reads length: 151

Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150

===== Before start started.

===== Assembling started.

===== K21 started.

== Running: /Users/pamluka/Desktop/programs_bioinformatics/SPAdes-3.15.4/bin/spades-core /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/K21/configs/config.info

0:00:00.000 1M / 6M INFO General (main.cpp : 99) Loaded config from /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/K21/configs/config.info 0:00:00.000 1M / 6M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb 0:00:00.000 1M / 6M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 1M / 6M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.000 1M / 6M INFO General (main.cpp : 109) Assembling dataset (/Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/dataset.info) with K=21 0:00:00.000 1M / 6M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 1M / 6M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.000 1M / 6M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.000 1M / 6M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.000 1M / 6M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.000 1M / 6M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.000 1M / 6M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.000 1M / 6M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.021 21M / 21M ERROR General (paired_readers.cpp : 39) The number of left read-pairs is larger than the number of right read-pairs 0:00:00.021 21M / 21M ERROR General (paired_readers.cpp : 41) Unequal number of read-pairs detected in the following files: /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq

== Error == system call for: "['/Users/pamluka/Desktop/programs_bioinformatics/SPAdes-3.15.4/bin/spades-core', '/Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/K21/configs/config.info']" finished abnormally, OS return value: 2 None

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 pr params.txt ovide us with params.txt and spades.log files from the output directory. spades.log

SPAdes log can be found here: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/spades.log

spades.log

Command line: /Users/pamluka/Desktop/programs_bioinformatics/SPAdes-3.15.4/spades.py -o /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly --only-assembler -1 /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq -2 /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq --pe1-1 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq --pe1-2 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq

System information: SPAdes version: 3.15.4 Python version: 3.9.7 OS: macOS-10.16-x86_64-i386-64bit

Output dir: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF

Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq', '/Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq'] right reads: ['/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq', '/Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq'] interlaced reads: not specified single reads: not specified 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: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/tmp Threads: 16 Memory limit (in Gb): 250

======= SPAdes pipeline started. Log can be found here: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/spades.log

/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq: max reads length: 151 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq: max reads length: 151 /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq: max reads length: 151 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq: max reads length: 151

Reads length: 151

Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150

===== Before start started.

===== Assembling started.

===== K21 started.

== Running: /Users/pamluka/Desktop/programs_bioinformatics/SPAdes-3.15.4/bin/spades-core /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/K21/configs/config.info

0:00:00.000 1M / 6M INFO General (main.cpp : 99) Loaded config from /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/K21/configs/config.info 0:00:00.000 1M / 6M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb 0:00:00.000 1M / 6M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 1M / 6M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.000 1M / 6M INFO General (main.cpp : 109) Assembling dataset (/Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/dataset.info) with K=21 0:00:00.000 1M / 6M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 1M / 6M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.000 1M / 6M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.000 1M / 6M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.000 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.000 1M / 6M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.000 1M / 6M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.000 1M / 6M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.000 1M / 6M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.021 21M / 21M ERROR General (paired_readers.cpp : 39) The number of left read-pairs is larger than the number of right read-pairs 0:00:00.021 21M / 21M ERROR General (paired_readers.cpp : 41) Unequal number of read-pairs detected in the following files: /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq

== Error == system call for: "['/Users/pamluka/Desktop/programs_bioinformatics/SPAdes-3.15.4/bin/spades-core', '/Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/K21/configs/config.info']" finished abnormally, OS return value: 2 None

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/pamluka/Desktop/UNGSM/sample_1/spades_assembly/spades.log

Thank you for using SPAdes!

params.txt

Command line: /Users/pamluka/Desktop/programs_bioinformatics/SPAdes-3.15.4/spades.py -o /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly --only-assembler -1 /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq -2 /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq --pe1-1 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq --pe1-2 /Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq

System information: SPAdes version: 3.15.4 Python version: 3.9.7 OS: macOS-10.16-x86_64-i386-64bit

Output dir: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF

Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq', '/Users/pamluka/Desktop/UNGSM/sample_1/reads_R1_trimmed.fastq'] right reads: ['/Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq', '/Users/pamluka/Desktop/UNGSM/sample_1/reads_R2_trimmed.fastq'] interlaced reads: not specified single reads: not specified 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: /Users/pamluka/Desktop/UNGSM/sample_1/spades_assembly/tmp Threads: 16 Memory limit (in Gb): 250

SPAdes version

Spades Verion 3.15.4

Operating System

MacOS Monterey 12.6.5

Python Version

No response

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 1 year ago

Hello

The log clearly reads:

0:00:00.021 21M / 21M ERROR General (paired_readers.cpp : 41) Unequal number of read-pairs detected in the following files: /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R1.fastq /Users/pamluka/Desktop/UNGSM/sample_1/unpaired_R2.fastq

Your left and right reads should match. Unpaired reads after trimming are single and should be provided as such