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Old 06-12-2019, 01:58 AM   #1
Location: Germany

Join Date: Apr 2018
Posts: 14
Default Assembly with trimmed FASTQ files fail


spades is working fine when I am using untrimmed fastq files.

I am using Trimmomatic to trim reads (SLIDINGWINDOW:30:20) and used the generated "output_forward_paired.fq.gz" and "output_reverse_paired.fq.gz" for assembly by Spades.

However, when using these files, no scaffolds.fasta file is generated and spades shows the following warnings:

======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:
* 0:00:38.523 48M / 6G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable
* 0:01:00.438 132M / 7G WARN General (pair_info_count.cpp : 342) Unable to estimate insert size for paired library #0
* 0:01:00.438 132M / 7G WARN General (pair_info_count.cpp : 348) None of paired reads aligned properly. Please, check orientation of your read pairs.
* 0:01:00.785 132M / 7G WARN General (repeat_resolving.cpp : 63) Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
How may I solve this issue? Why do I get these warnings when using trimmed reads?
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