Error during spades assembly

[toddmclay]

Hello,

I have been trying to run GetOrganelle and am running into an error in the Spades assembly -

'2018-04-13 14:11:36,749 - ERROR: Error in SPAdes:
== Error == system call for: "['/apps/spades/3.11.1/bin/spades', '/flush1/mcl300/Alangium/GetOrganelle/Alangium_output4/filtered_spades/K95/configs/config.info']" finished abnormally, err code: -8\n\n
2018-04-13 14:11:36,749 - ERROR: Assembling failed.

This error occurs in the final kmer assembly, no matter how many kmer values I try. For example, if I set kmer = 75,85,95, it will fail at 95. If I set k = 75, 85, it will fail at 85. If I set k=75, it won't run at all.

Here is the code I am using to run the software:

python /home/mcl300/GetOrganelle/get_organelle_reads.py \
-1 /home/mcl300/Alangium/13_4T_R1.fastq -2 /home/mcl300/Alangium/13_4T_R2.fastq \
-s /home/mcl300/Alangium/MG524996.fasta -w 103 -o Alangium_output4 \
-R 10 -F -k 75,85,95 -P 0 --out-per-round --no-remove-duplicates --verbose --spades-options "--memory 1000 --threads 10 --phred-offset 33"

Any help would be appreciated.

Cheers,
Todd

[Kinggerm]

Hi Todd,

Can you post the complete log files of GetOrganelle and SPAdes here or send them to my email?

Cheers,
Jianjun

[toddmclay]

Hi Jianjun,

Thanks for your response. I've attached the log files for both GetOrganelle and Spades.

Cheers,
Todd

GetOrganelle.15134537.txt
spades.log

[Kinggerm]

Hi Todd,

I took a look at your log files. I'm sorry I cannot figure out why SPAdes crashes. I googled for SPAdes with "err code: -8" but find nothing related.
Could you try your data with another server? I can see that your data is small enough to be run on most linux/Mac laptop with GetOrganelle, which should not take more than 30 minutes.

By the way, -w 103 could be too large for a small dataset, but, since you still have plenty of reads captured at this moment, you don't really need to change it. But if you find your plastome contigs to be unconnected in the graph, try -w 95 or a smaller value.

Best,
Jianjun

[toddmclay]

Hi Jianjun,

I wonder if 'error code: -8' is a default linux error code? I will try it on another computer and see if it completes. I have run several other softwares which include spades and have not run into any errors.

Thanks for your suggestions,,
Todd

[Kinggerm]

Hi Todd,

Have you went through it?

Best,
Jianjun