spades finished abnormally, err code -6

[asavelar]

The assembly finished but I got this message:

== ERRORs:

• system call for: "['/Volumes/ExternalHD500/SPAdes-3.13.0-Darwin/bin/spades-core', '/Volumes/ExternalHD500/spades_K21_25_33_55_C1/K55/configs/config.info']" finished abnormally, err code: -6

Why did this happen? can I change the parameters somehow? I am doing a de novo assembly on RNAseq contigs, 75bp reads.

Warning log: === Error correction and assembling warnings:

• 0:29:55.522 6G / 8G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable
• 0:30:28.690 7G / 8G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 11
• 0:30:28.692 7G / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 11
• 0:12:40.540 7G / 9G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 3
• 0:12:40.541 7G / 9G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 3
• 0:24:08.907 6G / 8G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2
• 0:24:08.908 6G / 8G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 ======= Warnings saved to /Volumes/ExternalHD500/spades_K21_25_33_55_C1/warnings.log

[asl]

Hello

Thank you for your interest in SPAdes.

Please attach the files that were mentioned just two lines below the ones you copied (and before the gihub link).

[asavelar]

warnings.log spades.log

[asl]

How much free RAM is available for your SPAdes job?

[asavelar]

Mac I am using has 128 GB, not running anything else at the same time. Did not limit the RAM for the task, but I am not sure if it has a default limit set up that I have to modify.

[peritob]

Hi, and thanks for your software. I have a similar issue to this one and am hoping there is a solution. I ran the following script with corrected files.

spades.py -t 24 -m 400 -o /scratch/pumpkin/ref/ --only-assembler --trusted-contigs /project/pumpkin/Jacob/genome.fa --pe1-1 /scratch/pumpkin/WSM1_HGMV2DSXX_ATCCACTG-AGGTGCGT_L001_R1.fastq.00.0_0.cor.fastq --pe1-2 /scratch/pumpkin/WSM1_HGMV2DSXX_ATCCACTG-AGGTGCGT_L001_R2.fastq.00.0_0.cor.fastq

======= SPAdes pipeline finished abnormally and WITH WARNINGS!

=== Error correction and assembling warnings:

4:58:48.825 20G / 44G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly ======= Warnings saved to /scratch/pumpkin/ref/warnings.log === ERRORs:

system call for: "['/usr/local/spades/3.12.0/bin/spades-core', '/scratch/pumpkin/ref/K77/configs/config.info']" finished abnormally, err code: -6

thanks for your help,

Peri

spades.log params.txt warnings.log.txt

[asl]

The log reads:

spades-core: /usr/local/src/SPADES/SPAdes-3.12.0/src/common/sequence/sequence.hpp:70: void Sequence::InitFromNucls(const S&, bool) [with S = std::__cxx11::basic_string<char>]: Assertion `is_dignucl(s[0]) || is_nucl(s[0])' failed.

So it seems you're having non-ACTGN symbols in your contig sequences. This is not supported. Please open new issues for new problems – do not hunt old ones that looks "similar" to you.

[bioramg]

Hi, Thank you for developing SPAdes for hybrid assembly.

I tried to assemble Illumina pair-end with Oxford Nanopore Sequence for plant mitochondrial genome assembly. Before carried out, I used BBMAP to trim adapters and normalize Illumina data. I have used the commands for trim adapters: bbmap$ ./bbduk.sh -Xmx1g in=read1.fastq in2=read2.fastq out=trim_read1.fastq out2=trim_read2.fastq ktrim=r k=23 mink=11 hdist=1 ref=resources/adapters.fa tbo tpe

for normalize: $./bbnorm.sh in=trim_read1.fastq in2=trim_read2.fastq out=norm_read1.fastq out2=norm_rread2.fastq target=100 min=5

Then, I used these Illumina pair-end reads with Oxford nanopore and the commands as follows: $ ./spades.py -k 99 --pe1-1 norm_read1.fastq --pe1-2 norm_read2.fastq --nanopore nano_read.fastq --careful --cov-cutoff 90 -o hybrid_assembly -m 188.

When I run using this command, I have got an error message as: ======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:

• 8:48:41.078 34G / 56G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable
• 8:48:41.472 34G / 56G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 22
• 8:48:41.477 34G / 56G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 22

I am herewith enclosing spades.log and warning.log files for your reference. Please find and suggest me what could be the problem and how to solve it...

spades.log warnings.log

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