Assembly finished but output contig file is empty
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Entering edit mode
2.1 years ago
tchow5 • 0

Hi everyone,

I'm a beginner using spades 3.11.0 since March2019 , trying to practice doing some assemblies via getting SRA files from papers that i'm interested in.

What I have done:

  1. Pulled SRA/ERR files using: curl -O ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/ERR/ERR238/ERR2383823/ERR2383823.sra

  2. fastq-dump --split-files --split-spot --skip-technical --minReadLen 64 --defline-seq @$ac.$si --defline-qual "+" ./ERR2383823.sra

  3. fastq_pair ERR2383823_1.fastq ERR2383823_2.fastq

  4. spades.py --pe1-1 ERR2383823_1.fastq.paired.fq --pe1-2 ERR2383823_2.fastq.paired.fq -o ERR2383823_spades

From my previous experience I have never encounter this issue. The program runs fine but then all the contigs.fasta output are very small and QUAST said: ERROR! None of the assembly files contains correct contigs. Please, provide different files or decrease --min-contig threshold.

Below is the warning messages I keep getting using different files. === Error correction and assembling warnings:

0:00:07.370 96M / 8G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable

0:00:09.449 100M / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 27

0:00:24.870 188M / 8G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 3

0:00:15.447 380M / 8G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2

0:00:15.448 380M / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2

0:00:21.646 408M / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 37

0:00:25.948 432M / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 39

0:00:26.538 444M / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 36

0:00:43.218 124M / 8G WARN General (pair_info_count.cpp : 355) Estimated mean insert size 253 is very small compared to read length 301

Would anybody know how to resolve this issue or any errors I should be aware of?

Assembly Spades sequencing • 682 views
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