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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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spades error #255 unequal amount of reads #1318

Closed ainurftn closed 1 week ago

ainurftn commented 1 week ago

Description of bug

I cannot completed my spades operation because it says the files have unequal amount of reads. I have googled on how to solve the problem & some of them suggested using fastq-pair but it still does not work.

fastq_pair /home/colfax/Documents/AINUR/TK/TK_1unmapped.fastq /home/colfax/Documents/AINUR/TK/TK_2unmapped.fastq Writing the paired reads to /home/colfax/Documents/AINUR/TK/TK_1unmapped.fastq.paired.fq and /home/colfax/Documents/AINUR/TK/TK_2unmapped.fastq.paired.fq. Writing the single reads to /home/colfax/Documents/AINUR/TK/TK_1unmapped.fastq.single.fq and /home/colfax/Documents/AINUR/TK/TK_2unmapped.fastq.single.fq Left paired: 0 Right paired: 0 Left single: 16723329 Right single: 17017982

I am confused as why the paired reads are 0. Please suggest me ways to match the paired reads.

spades.log

Documents/AINUR/TK/TK_1unmapped.fastq.single.fq and /home/colfax/Documents/AINUR/TK/TK_2unmapped.fastq.single.fq contain unequal amount of reads

== Error == system call for: "['/home/colfax/anaconda3/share/spades-3.13.0-0/bin/spades-hammer', '/home/colfax/Documents/AINUR/TK/spades_TK/corrected/configs/config.info']" finished abnormally, err code: 255

params.txt

Command line: /home/colfax/anaconda3/bin/spades.py -k 127 --careful -1 /home/colfax/Documents/AINUR/TK/TK_1unmapped.fastq.single.fq -2 /home/colfax/Documents/AINUR/TK/TK_2unmapped.fastq.single.fq -o /home/colfax/Documents/AINUR/TK/spades_TK -t 16

System information: SPAdes version: 3.13.0 Python version: 3.8.5 OS: Linux-6.5.0-21-generic-x86_64-with-glibc2.10

Output dir: /home/colfax/Documents/AINUR/TK/spades_TK Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/home/colfax/Documents/AINUR/TK/TK_1unmapped.fastq.single.fq'] right reads: ['/home/colfax/Documents/AINUR/TK/TK_2unmapped.fastq.single.fq'] 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: [127] Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: /home/colfax/Documents/AINUR/TK/spades_TK/tmp Threads: 16 Memory limit (in Gb): 125

SPAdes version

SPAdes 4.0.0

Operating System

Linux

Python Version

No response

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 1 week ago

Well, the error message is pretty exact: your input reads are corrupted, left ones should correspond to right ones. SPAdes cannot fix your broken read for you, you need to ensure the input if correct. If you are using some kind of pre-processing or filtering, for example, make sure the process is paired-end aware.