mtDNA error

[Syzall]

Hello Dr Jin.
I'm trying to assemble some bird's mtDNA and received the following error:

GetOrganelle v1.7.4.1

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 3.8.10 (default, May 26 2023, 14:05:08) [GCC 9.4.0]
PLATFORM: Linux arapaima 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.4.1; numpy 1.24.4; sympy 1.12; scipy 1.10.1; psutil 5.9.5
DEPENDENCIES: Bowtie2 2.4.5; SPAdes 3.13.1; Blast 2.14.0
GETORG_PATH=/home/davi/.GetOrganelle
SEED DB: animal_mt 0.0.1
LABEL DB: animal_mt 0.0.1
WORKING DIR: /home/davi
/home/davi/.local/bin/get_organelle_from_reads.py -1 SRR12555060_Target_enrichment_of_UCEs_and_exons_from_Neopelma_chrysolophum_Neopel_chrlop_F395453__1.fastq.gz -2 SRR12555060_Target_enrichment_of_UCEs_and_exons_from_Neopelma_chrysolophum_Neopel_chrlop_F395453__2.fastq.gz -R 30 -k 21,45,65,85,105 -F animal_mt -o Neopelma_chrysolophum_mt_out --max-read inf --reduce-reads-for-coverage inf --overwrite

2023-07-05 18:47:31,799 - INFO: Pre-reading fastq ...
2023-07-05 18:47:31,799 - INFO: Unzipping reads file: SRR12555060_Target_enrichment_of_UCEs_and_exons_from_Neopelma_chrysolophum_Neopel_chrlop_F395453__1.fastq.gz (483114512 bytes)
2023-07-05 18:47:44,277 - INFO: Unzipping reads file: SRR12555060_Target_enrichment_of_UCEs_and_exons_from_Neopelma_chrysolophum_Neopel_chrlop_F395453__2.fastq.gz (396828512 bytes)
2023-07-05 18:47:54,717 - INFO: Counting read qualities ...
2023-07-05 18:47:54,842 - INFO: Identified quality encoding format = Illumina 1.8+
2023-07-05 18:47:54,842 - INFO: Phred offset = 33
2023-07-05 18:47:54,843 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2023-07-05 18:47:54,918 - INFO: Mean error rate = 0.0317
2023-07-05 18:47:54,919 - INFO: Counting read lengths ...
2023-07-05 18:48:13,808 - INFO: Mean = 89.0 bp, maximum = 100 bp.
2023-07-05 18:48:13,808 - INFO: Reads used = 5850434+5850434
2023-07-05 18:48:13,808 - INFO: Pre-reading fastq finished.

2023-07-05 18:48:13,808 - INFO: Making seed reads ...
2023-07-05 18:48:13,809 - INFO: Seed bowtie2 index existed!
2023-07-05 18:48:13,809 - INFO: Mapping reads to seed bowtie2 index ...
2023-07-05 18:53:22,726 - INFO: Mapping finished.
2023-07-05 18:53:22,726 - INFO: Seed reads made: Neopelma_chrysolophum_mt_out/seed/animal_mt.initial.fq (482542 bytes)
2023-07-05 18:53:22,728 - INFO: Making seed reads finished.

2023-07-05 18:53:22,728 - INFO: Checking seed reads and parameters ...
2023-07-05 18:53:22,728 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-07-05 18:53:22,728 - INFO: If the result graph is not a circular organelle genome,
2023-07-05 18:53:22,728 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2023-07-05 18:53:25,901 - INFO: Pre-assembling mapped reads ...
2023-07-05 18:53:27,049 - INFO: Retrying with more reads ..
2023-07-05 18:57:05,254 - WARNING: Pre-assembling failed. The estimations for animal_mt-hitting base-coverage and word size may be misleading.
2023-07-05 18:57:22,209 - INFO: Estimated animal_mt-hitting base-coverage = 62.33
2023-07-05 18:57:22,660 - INFO: Estimated word size(s): 42
2023-07-05 18:57:22,660 - INFO: Setting '-w 42'
2023-07-05 18:57:22,660 - INFO: Setting '--max-extending-len inf'
2023-07-05 18:57:22,752 - INFO: Checking seed reads and parameters finished.

2023-07-05 18:57:22,753 - INFO: Making read index ...
2023-07-05 18:59:44,733 - INFO: Mem 1.36 G, 1479859 candidates in all 11700868 reads
2023-07-05 18:59:44,772 - INFO: Pre-grouping reads ...
2023-07-05 18:59:44,772 - INFO: Setting '--pre-w 42'
2023-07-05 18:59:45,038 - INFO: Mem 1.195 G, 200000/322918 used/duplicated
2023-07-05 19:00:02,281 - INFO: Mem 1.782 G, 5800 groups made.
2023-07-05 19:00:03,869 - INFO: Making read index finished.

2023-07-05 19:00:03,870 - INFO: Extending ...
2023-07-05 19:00:03,870 - INFO: Adding initial words ...
2023-07-05 19:00:03,941 - INFO: AW 97397
2023-07-05 19:00:13,594 - INFO: Round 1: 1479859/1479859 AI 27104 AW 682461 Mem 1.069
2023-07-05 19:00:23,822 - INFO: Round 2: 1479859/1479859 AI 49477 AW 1165096 Mem 1.07
2023-07-05 19:00:33,817 - INFO: Round 3: 1479859/1479859 AI 56713 AW 1327850 Mem 1.101
2023-07-05 19:00:43,435 - INFO: Round 4: 1479859/1479859 AI 57662 AW 1348306 Mem 1.101
2023-07-05 19:00:53,024 - INFO: Round 5: 1479859/1479859 AI 57673 AW 1348626 Mem 1.101
2023-07-05 19:01:02,592 - INFO: Round 6: 1479859/1479859 AI 57673 AW 1348626 Mem 1.101
2023-07-05 19:01:02,592 - INFO: No more reads found and terminated ...
2023-07-05 19:01:22,163 - INFO: Extending finished.

2023-07-05 19:01:22,584 - INFO: Separating extended fastq file ...
2023-07-05 19:01:24,124 - INFO: Setting '-k 21,45,65,85'
2023-07-05 19:01:24,125 - INFO: Assembling using SPAdes ...
2023-07-05 19:01:24,156 - INFO: spades.py -t 1 --phred-offset 33 -1 Neopelma_chrysolophum_mt_out/extended_1_paired.fq -2 Neopelma_chrysolophum_mt_out/extended_2_paired.fq --s1 Neopelma_chrysolophum_mt_out/extended_1_unpaired.fq --s2 Neopelma_chrysolophum_mt_out/extended_2_unpaired.fq -k 21,45,65,85 -o Neopelma_chrysolophum_mt_out/extended_spades
2023-07-05 19:01:24,546 - WARNING: Assembling exited halfway.

2023-07-05 19:01:24,953 - ERROR:
Traceback (most recent call last):
File "/home/davi/.local/bin/get_organelle_from_reads.py", line 4109, in main
slim_stat_list, ignore_k = slim_spades_result(
File "/home/davi/.local/bin/get_organelle_from_reads.py", line 3263, in slim_spades_result
if max(kmer_values) <= ignore_kmer_res:
ValueError: max() arg is an empty sequence

Thank you in advance for your time.

[JianjunJin]

Hi, please try to update your SPAdes (see #198 ) or reinstall SPAdes (see the related question at FAQ).
Besides, updating your GetOrganelle to the latest version is highly recommended!

Let me know.