running SPAdes on paired end reads of different length didn't generate scaffolds.fasta #1231
Description
Description of bug
I used spades to assemble paired end reads that aren't of the same length, my R1 file contains 50bp reads and my R2 file contains 26bp reads. The reads are in the same order in both files.
I got a contigs.fasta file in my results but didn't get scaffolds.fasta, and I wanted to ask why? In addition, does the lack of scaffolds.fasta file indicate a bigger problem and my results (the contigs.fasta file) aren't reliable?
I got this errors in my log file, but I didn't understand if they are related to my problem. or how I can fix them:
=== Error correction and assembling warnings:
- 0:00:57.431 58M / 581M WARN General (pair_info_count.cpp : 358) Unable to estimate insert size for paired library #0
- 0:00:57.431 58M / 581M WARN General (pair_info_count.cpp : 364) None of paired reads aligned properly. Please, check orientation of your read pairs.
- 0:00:57.431 58M / 581M WARN General (repeat_resolving.cpp : 81) Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
======= Warnings saved to /sci/backup/morani/lab/Projects/Aluma/Hadza_genomic/subsampled_results/spades_results/paired/ERR9631799_sub_samp_2.5M_50_26bp_spades_paired_output/warnings.log
Thank you
spades.log
params.txt
SPAdes version
3.15.5
Operating System
Linux-5.10.104-aufs-3-x86_64-with-debian-10.10
Python Version
No response
Method of SPAdes installation
binaries
No errors reported in spades.log
- Yes