Assembling exited halfway - ERROR: No valid assembly graph found

[JianjunJin]

Take the liberty to borrow the post owner's place. I want to ask where my error occurred. It always occurs No valid Assembly graph found.@Kinggerm
First, the code I used:get_organelle_from_reads.py -1 /home/mxx/anaconda3/envs/get/BR1_FDMS210380612-1a_1.clean.fq.gz -2 /home/mxx/anaconda3/envs/get/BR1_FDMS210380612-1a_2.clean.fq.gz -o test5 -R 32 -t 64 -F animal_mt --reduce-reads-for-coverage inf --max-reads inf
log file:
get_org.log.txt
spades.log
Please take a look at this when convenient to yourself.

Originally posted by @9326xiaoxiao in #116 (comment)

[JianjunJin]

Your issue is different from issue116. Please note that the spades assembly step exited almost immediately after the start. So you troubleshoot your environment to run spades normally.

The spades.log you provides is not the right one. Please provide the spades.log file under test5/extend_spades if it existed.

[o-william-white]

I think this may be a conda dependency issue.

With spades v3.13.0 the log looks like this

Command line: /mnt/shared/scratch/owhite/apps/conda/envs/getorgelle_conda_env/bin/spades.py     -t      1       --phred-offset  33      -1      /mnt/shared/home/owhite/test/getorganelle/results_directory/extended_1_paired.fq -2      /mnt/shared/home/owhite/test/getorganelle/results_directory/extended_2_paired.fq        --s1    /mnt/shared/home/owhite/test/getorganelle/results_directory/extended_1_unpaired.fq       --s2    /mnt/shared/home/owhite/test/getorganelle/results_directory/extended_2_unpaired.fq      -k      21,55,85,115    -o      /mnt/shared/home/owhite/test/getorganelle/results_directory/extended_spades

System information:
  SPAdes version: 3.13.0
  Python version: 3.10.6
  OS: Linux-4.18.0-372.26.1.el8_6.x86_64-x86_64-with-glibc2.28

Output dir: /mnt/shared/home/owhite/test/getorganelle/results_directory/extended_spades
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:

With spades version 3.15.5 it works as expected.

With my conda installation conda (```conda create --name getorganelle getorganelle````) I get spades 3.15.5. But with conda I get 3.13.0

[FuXiaogang-KIB]

Thanks for Ollie White's comments. This is the solution to the problem! Just update your SPAdes to version 3.15.5 (conda update SPAdes). It will work normally.

[Rajaratnam1234]

Hi, tried to do de novo assembly for Arabidopsis test data, during the process assembly existed halfway and received an error; No valid graph found.
I have attached the log file herewith. Could you please help me to resolve the issue

get_org.log.txt

[JianjunJin]

@Rajaratnam1234
Have you tried to install SPAdes from the source?

[Rajaratnam1234]

Thank you for your response. There was an error in python. I re_installed the package. Now assembling is working properly!

…

On Mon, 24 Jul 2023, 6:39 am JianJun Jin, ***@***.***> wrote: @Rajaratnam1234 <https://github.com/Rajaratnam1234> Have you tried to install SPAdes from the source? — Reply to this email directly, view it on GitHub <#198 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBMU4OB7A4B442F7CIHOUEDXRXDLVANCNFSM6AAAAAAQYKKKZQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[timurrxxcd]

@JianjunJin I encountered similar issue while assembling cp genome, but it's not because if version of SPAdes or python. I got only extended_1_paired.fq, extended_2_paired.fq, extended_1_unpaired.fq, extended_2_unpaired.fq files as result. I think it maybe due to sequencing (632 MB and 670 MB forward and reverse reads) process. do you think it is impossible to assemble it? here is log file:

_2024-07-26 17:04:39,912 - INFO: Separating extended fastq file ...
2024-07-26 17:04:55,127 - INFO: Setting '-k 21,45,65,85,105'
2024-07-26 17:04:55,127 - INFO: Assembling using SPAdes ...
2024-07-26 17:04:55,185 - INFO: spades.py -t 1 --phred-offset 33 -1 output_T7_1.fq.gz/extended_1_paired.fq -2 output_T7_1.fq.gz/extended_2_paired.fq --s1 output_T7_1.fq.gz/extended_1_unpaired.fq --s2 output_T7_1.fq.gz/extended_2_unpaired.fq -k 21,45,65,85,105 -o output_T7_1.fq.gz/extended_spades
2024-07-26 22:39:05,172 - INFO: Insert size = 315.28, deviation = 67.2329, left quantile = 232, right quantile = 402
2024-07-26 22:39:05,176 - INFO: Assembling finished.

2024-07-26 22:39:12,588 - ERROR: Slimming output_T7_1.fq.gz/extended_spades/K105/assembly_graph.fastg failed. Please check output_T7_1.fq.gz/extended_spades/K105/slim.log.txt for details.
2024-07-26 22:39:12,589 - ERROR: No valid assembly graph found!
2024-07-26 22:39:12,589 - WARNING: This might due to a damaged dependency, to unreasonable seed/parameter choices, or to a bug.
2024-07-26 22:39:12,589 - INFO: Please first search similar issues at https://github.com/Kinggerm/GetOrganelle/issues, then leave your message following the same issue, or open an issue at https://github.com/Kinggerm/GetOrganelle/issues if it is new, Please always attach the get_org.log.txt file.

Total cost 25550.39 s
Thank you!

[JianjunJin]

@timurrxxcd

• Please always attach the complete log file for troubleshooting.
• Please open a new issue because it differs from the current one. In the issue description, please list the files in extended_spades and extended_spades/K105. Please attach the output_T7_1.fq.gz/extended_spades/K105/slim.log.txt file as well, if applicable. Thanks!