ERROR: slimming the pre-assembled graph failed

[ByMansi]

I have run GetOrganelle to assemble my single sample using Illumina paired end data. The process was not completed. Please find the content of logfile "get_org.log.txt":

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 3.7.6 (default, Jan 8 2020, 19:59:22) [GCC 7.3.0]
PLATFORM: Linux node3 5.15.0-56-generic #62~20.04.1-Ubuntu SMP Tue Nov 22 21:24:20 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.18.1; sympy 1.5.1; scipy 1.4.1; psutil 5.6.7
DEPENDENCIES: Bowtie2 2.5.0; SPAdes 3.15.4; Blast 2.9.0
GETORG_PATH=/home/user1/.GetOrganelle
SEED DB: embplant_pt 0.0.1; embplant_mt 0.0.1
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /GetOrganelle/get_organelle_from_reads.py -1 R1.fq -2 R2.fq -o output_GetOrganelle -F embplant_pt -R 5 -t 60 --which-spades /SPAdes-3.15.4/bin --reduce-reads-for-coverage inf --max-reads inf2023-05-11 14:36:25,929 - INFO: Pre-reading fastq ...
2023-05-11 14:36:57,142 - INFO: Counting read qualities ...
2023-05-11 14:36:57,872 - INFO: Identified quality encoding format = Sanger
2023-05-11 14:36:57,872 - INFO: Phred offset = 33
2023-05-11 14:36:57,874 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2023-05-11 14:36:57,903 - INFO: Mean error rate = 0.0022
2023-05-11 14:36:57,904 - INFO: Counting read lengths ...
2023-05-11 14:37:26,163 - INFO: Mean = 141.7 bp, maximum = 151 bp.
2023-05-11 14:37:26,163 - INFO: Reads used = 13145851+13145851
2023-05-11 14:37:26,163 - INFO: Pre-reading fastq finished.2023-05-11 14:37:26,163 - INFO: Making seed reads ...
2023-05-11 14:37:26,249 - INFO: Seed bowtie2 index existed!
2023-05-11 14:37:26,249 - INFO: Mapping reads to seed bowtie2 index ...
2023-05-11 14:40:24,566 - INFO: Mapping finished.
2023-05-11 14:40:24,570 - INFO: Seed reads made: output_GetOrganelle/seed/embplant_pt.initial.fq (171476664 bytes)
2023-05-11 14:40:24,576 - INFO: Making seed reads finished.2023-05-11 14:40:24,576 - INFO: Checking seed reads and parameters ...
2023-05-11 14:40:24,576 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-05-11 14:40:24,577 - INFO: If the result graph is not a circular organelle genome,
2023-05-11 14:40:24,577 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2023-05-11 14:40:44,506 - INFO: Pre-assembling mapped reads ...
2023-05-11 14:44:09,851 - ERROR: slimming the pre-assembled graph failed.
2023-05-11 14:44:11,301 - INFO: Pre-assembling mapped reads finished.
2023-05-11 14:44:11,301 - INFO: Estimated embplant_pt-hitting base-coverage = 619.63
2023-05-11 14:44:11,590 - INFO: Estimated word size(s): 106
2023-05-11 14:44:11,590 - INFO: Setting '-w 106'
2023-05-11 14:44:11,590 - INFO: Setting '--max-extending-len inf'
2023-05-11 14:44:13,166 - INFO: Checking seed reads and parameters finished.2023-05-11 14:44:13,166 - INFO: Making read index ...
2023-05-11 14:46:37,913 - INFO: Mem 5.265 G, 21882822 candidates in all 26291702 reads
2023-05-11 14:46:37,914 - INFO: Pre-grouping reads ...
2023-05-11 14:46:37,914 - INFO: Setting '--pre-w 106'
2023-05-11 14:46:39,456 - INFO: Mem 5.187 G, 200000/1509815 used/duplicated
2023-05-11 14:46:54,949 - INFO: Mem 6.78 G, 3441 groups made.
2023-05-11 14:46:59,918 - INFO: Making read index finished.2023-05-11 14:46:59,918 - INFO: Extending ...
2023-05-11 14:46:59,918 - INFO: Adding initial words ...
2023-05-11 14:47:09,263 - INFO: AW 3883278
2023-05-11 14:48:58,329 - INFO: Round 1: 21882822/21882822 AI 419224 AW 4534428 Mem 2.24
2023-05-11 14:50:40,419 - INFO: Round 2: 21882822/21882822 AI 446415 AW 5063906 Mem 2.365
2023-05-11 14:52:27,933 - INFO: Round 3: 21882822/21882822 AI 888523 AW 12829026 Mem 3.559
2023-05-11 14:54:27,210 - INFO: Round 4: 21882822/21882822 AI 2173906 AW 32270036 Mem 7.121
2023-05-11 14:56:14,692 - INFO: Round 5: 21882822/21882822 AI 2657623 AW 42042964 Mem 9.815
2023-05-11 14:56:14,693 - INFO: Hit the round limit 5 and terminated ...
2023-05-11 14:57:14,760 - INFO: Extending finished.2023-05-11 14:57:15,370 - INFO: Separating extended fastq file ...
2023-05-11 14:57:27,020 - INFO: Setting '-k 21,55,85,115'
2023-05-11 14:57:27,020 - INFO: Assembling using SPAdes ...
2023-05-11 14:57:27,093 - INFO: /SPAdes-3.15.4/bin/spades.py -t 60 --phred-offset 33 -1 output_GetOrganelle/extended_1_paired.fq -2 output_GetOrganelle/extended_2_paired.fq --s1 output_GetOrganelle/extended_1_unpaired.fq --s2 output_GetOrganelle/extended_2_unpaired.fq -k 21,55,85,115 -o output_GetOrganelle/extended_spades

Please help me to solve this.

[JianjunJin]

You need to follow the template for posting an issue and provide the complete log file.

[Kinggerm]

The issue is literally what the log says. Please increase the data input