Error - animal mitochondrial genome

[Yeon-Jay]

Dear Dr. Jin,

I am trying to get mitochondrial genome of a beetle species, but have encountered errors.

Here's the log:

GetOrganelle v1.7.7.0

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.16 (default, Jan 17 2023, 09:28:58) [Clang 14.0.6 ]
PLATFORM: Darwin choeyeonjaeui-MacBook-Pro.local 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 x86_64 i386
PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.21.5; sympy 1.10.1; scipy 1.7.3
DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.15.5; Blast 2.6.0
GETORG_PATH=/Users/choiyeonjae/.GetOrganelle
SEED DB: animal_mt 0.0.1
LABEL DB: animal_mt 0.0.1
WORKING DIR: /Users/choiyeonjae
/opt/anaconda3/envs/python3.7/bin/get_organelle_from_reads.py -1 Tni_Male.decontam_1.fastq.gz -2 Tni_Male.decontam_2.fastq.gz -R 10 -F animal_mt -o animal_mt_out --overwrite

2023-07-27 14:38:01,265 - INFO: Pre-reading fastq ...
2023-07-27 14:38:01,265 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2023-07-27 14:38:01,361 - INFO: Tasting 100000+100000 reads ...
Error with running SPAdes: == Error == system call for: "['/usr/local/Cellar/spades/3.15.5/bin/spades-core', '/Users/choiyeonjae/animal_mt_out/check/1/animal_mt.check.fq.spades/K45/configs/config.info']" finished abnormally, OS return value: 2
2023-07-27 14:39:00,067 - INFO: Tasting 500000+500000 reads ...
2023-07-27 14:40:23,617 - INFO: Tasting 2500000+2500000 reads ...
2023-07-27 14:44:00,026 - INFO: Tasting 12500000+12500000 reads ...
2023-07-27 14:58:59,828 - INFO: Estimating reads to use finished.
2023-07-27 14:58:59,830 - INFO: Unzipping reads file: Tni_Male.decontam_1.fastq.gz (8226821569 bytes)
2023-07-27 15:00:04,753 - INFO: Unzipping reads file: Tni_Male.decontam_2.fastq.gz (8653863754 bytes)
2023-07-27 15:01:13,251 - INFO: Counting read qualities ...
2023-07-27 15:01:13,351 - INFO: Identified quality encoding format = Sanger
2023-07-27 15:01:13,351 - INFO: Phred offset = 33
2023-07-27 15:01:13,354 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2023-07-27 15:01:13,379 - INFO: Mean error rate = 0.0027
2023-07-27 15:01:13,380 - INFO: Counting read lengths ...
2023-07-27 15:04:47,907 - INFO: Mean = 151.0 bp, maximum = 151 bp.
2023-07-27 15:04:47,909 - INFO: Reads used = 117808289+117808289
2023-07-27 15:04:47,909 - INFO: Pre-reading fastq finished.

2023-07-27 15:04:47,909 - INFO: Making seed reads ...
2023-07-27 15:04:47,910 - INFO: Seed bowtie2 index existed!
2023-07-27 15:04:47,910 - INFO: Mapping reads to seed bowtie2 index ...
2023-07-27 15:57:07,847 - INFO: Mapping finished.
2023-07-27 15:57:07,848 - INFO: Seed reads made: animal_mt_out/seed/animal_mt.initial.fq (94235 bytes)
2023-07-27 15:57:07,849 - INFO: Making seed reads finished.

2023-07-27 15:57:07,849 - INFO: Checking seed reads and parameters ...
2023-07-27 15:57:07,849 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-07-27 15:57:07,850 - INFO: If the result graph is not a circular organelle genome,
2023-07-27 15:57:07,850 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2023-07-27 15:57:10,281 - INFO: Pre-assembling mapped reads ...
2023-07-27 15:57:12,918 - INFO: Pre-assembling mapped reads finished.
2023-07-27 15:57:12,918 - INFO: Estimated animal_mt-hitting base-coverage = 10.30
2023-07-27 15:57:13,141 - WARNING: Guessing that you are using too few data for assembling animal_mt!
2023-07-27 15:57:13,142 - WARNING: GetOrganelle is still trying ...
2023-07-27 15:57:13,142 - INFO: Estimated word size(s): 41
2023-07-27 15:57:13,142 - INFO: Setting '-w 41'
2023-07-27 15:57:13,142 - INFO: Setting '--max-extending-len inf'
2023-07-27 15:57:13,201 - INFO: Checking seed reads and parameters finished.

2023-07-27 15:57:13,201 - INFO: Making read index ...
2023-07-27 17:00:55,767 - INFO: 228287313 candidates in all 235616578 reads
2023-07-27 17:00:55,783 - INFO: Pre-grouping reads ...
2023-07-27 17:00:55,783 - INFO: Setting '--pre-w 41'
2023-07-27 17:03:34,653 - INFO: 200000/5827778 used/duplicated
2023-07-27 17:04:33,438 - INFO: 5318 groups made.
2023-07-27 17:09:20,048 - INFO: Making read index finished.

2023-07-27 17:09:20,054 - INFO: Extending ...
2023-07-27 17:09:20,057 - INFO: Adding initial words ...
2023-07-27 17:09:20,080 - INFO: AW 11820
2023-07-27 17:51:40,841 - INFO: Round 1: 9816342/228287313 AI 3897760 AW 201818670
2023-07-27 17:51:40,855 - INFO: Hit the words limit and terminated ...
2023-07-27 17:51:40,856 - WARNING: Terminated at an insufficient number of rounds, see '--max-n-words'/'--max-extending-len' for more.

The command was operated on iTerm2 (x86) to activate Rosetta 2.

I also attached the log file, which is missing "Error with running SPAdes: == Error ==  system call for: "['/usr/local/Cellar/spades/3.15.5/bin/spades-core', '/Users/choiyeonjae/animal_mt_out/check/1/animal_mt.check.fq.spades/K45/configs/config.info']" finished abnormally, OS return value: 2".

Can you help me please?

[get_org.log.txt](https://github.com/Kinggerm/GetOrganelle/files/12181508/get_org.log.txt)

[JianjunJin]

You may try to use a slightly larger words size (e.g. -w 65) and a seed database from a closely related species (-s close_sp_mt.fasta).

[Yeon-Jay]

Thank you. I think it was because my machine has insufficient RAM to cover this data.