asl
commented
4 years ago Hello
The log reads:
0:00:00.780 171M / 171M ERROR General (paired_readers.cpp : 41) Unequal number of read-pairs detected in the following files: /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_1.fastq.gz /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_2.fastq.gzSo your input reads are corrupted.
Hi
I am using unicycler to run hybrid assembly of a bacterium genome with both nanopore and illumina data. Spades ran into some issues, could anyone please help me figure out what is going on here?
My command : (base) campus-107-113:SJ003 dklabuser$ unicycler -1 SJ003_S12.R1.trimmed.fastq.gz -2 SJ003_S12.R2.trimmed.fastq.gz -s SJ003_S12.R1.trimmed.unpaired.fastq.gz -s SJ003_S12.R2.trimmed.unpaired.fastq.gz -l SJ003_filtered.fastq.gz --existing_long_read_assembly SJ003_unp.fasta --mode bold -o SJ003_bold -t 8
See spades_assembly/assembly/spades.log for more info below: Command line: /Users/dklabuser/miniconda3/bin/spades.py -o /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 8 --only-assembler -1 /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_1.fastq.gz -2 /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_2.fastq.gz --only-assembler -s /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_u.fastq.gz
System information: SPAdes version: 3.14.0 Python version: 3.7.4 OS: Darwin-19.2.0-x86_64-i386-64bit
Output dir: /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/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/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_1.fastq.gz'] right reads: ['/Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_2.fastq.gz'] interlaced reads: not specified single reads: ['/Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_u.fastq.gz'] merged reads: not specified Assembly parameters: k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127] 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/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/tmp Threads: 8 Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/spades.log
/Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_1.fastq.gz: max reads length: 301 /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_2.fastq.gz: max reads length: 281 /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_u.fastq.gz: max reads length: 301
Reads length: 301
===== Assembling started.
===== K27 started.
== Running: /Users/dklabuser/miniconda3/bin/spades-core /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/K27/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loaded config from /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/K27/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting SPAdes, built from refs/heads/is-update-spades-to-3.14.0, git revision 45f1eddeb4c895cea74e59e81ab8d523515af1f5 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 85) Assembling dataset (/Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/dataset.info) with K=27 0:00:00.000 4M / 4M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.000 4M / 4M INFO General (launch.hpp : 79) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.000 4M / 4M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.000 4M / 4M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.000 4M / 4M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.780 171M / 171M ERROR General (paired_readers.cpp : 39) The number of left read-pairs is larger than the number of right read-pairs 0:00:00.780 171M / 171M ERROR General (paired_readers.cpp : 41) Unequal number of read-pairs detected in the following files: /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_1.fastq.gz /Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/corrected_2.fastq.gz
== Error == system call for: "['/Users/dklabuser/miniconda3/bin/spades-core', '/Users/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/K27/configs/config.info']" finished abnormally, OS return value: 255
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/dklabuser/Desktop/Unresolved/SJ003/SJ003_bold/spades_assembly/assembly/spades.log
Thank you for using SPAdes!