GetOrganelle v1.7.6.1 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 3.9.5 (default, Nov 23 2021, 15:27:38) [GCC 9.3.0] PLATFORM: Linux administrador-dell-r630 5.15.0-58-generic #64~20.04.1-Ubuntu SMP Fri Jan 6 16:42:31 UTC 2023 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.6.1 DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.1; Blast 2.9.0 GETORG_PATH=/home/valery/.GetOrganelle SEED DB: animal_mt 0.0.0 LABEL DB: animal_mt 0.0.1 WORKING DIR: /home/valery/reads_mitogenomas/09-01-23/filtrado/resultado_filtrado /home/valery/./get_organelle_from_reads.py -1 test_1.fastq -2 test_2.fastq -R 10 -t 8 -F animal_mt -o ranita4_mt_out 2023-02-02 11:59:27,845 - ERROR: numpy/sympy/scipy not available! Disentangling disabled!! 2023-02-02 11:59:27,854 - INFO: Pre-reading fastq ... 2023-02-02 11:59:27,854 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf') 2023-02-02 11:59:27,867 - INFO: Tasting 100000+100000 reads ... 2023-02-02 12:00:30,374 - INFO: Tasting 500000+500000 reads ... 2023-02-02 12:00:43,271 - INFO: Estimating reads to use finished. 2023-02-02 12:00:58,356 - INFO: Counting read qualities ... 2023-02-02 12:00:58,537 - INFO: Identified quality encoding format = Sanger 2023-02-02 12:00:58,537 - INFO: Phred offset = 33 2023-02-02 12:00:58,539 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2023-02-02 12:00:58,660 - INFO: Mean error rate = 0.0149 2023-02-02 12:00:58,661 - INFO: Counting read lengths ... 2023-02-02 12:01:18,970 - INFO: Mean = 226.8 bp, maximum = 301 bp. 2023-02-02 12:01:18,971 - INFO: Reads used = 8309254+8309254 2023-02-02 12:01:18,971 - INFO: Pre-reading fastq finished. 2023-02-02 12:01:18,971 - INFO: Making seed reads ... 2023-02-02 12:01:18,971 - INFO: Seed bowtie2 index existed! 2023-02-02 12:01:18,971 - INFO: Mapping reads to seed bowtie2 index ... 2023-02-02 12:02:47,777 - INFO: Mapping finished. 2023-02-02 12:02:47,777 - INFO: Seed reads made: ranita4_mt_out/seed/animal_mt.initial.fq (1217674 bytes) 2023-02-02 12:02:47,778 - INFO: Making seed reads finished. 2023-02-02 12:02:47,778 - INFO: Checking seed reads and parameters ... 2023-02-02 12:02:47,778 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s). 2023-02-02 12:02:47,778 - INFO: If the result graph is not a circular organelle genome, 2023-02-02 12:02:47,778 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run. 2023-02-02 12:02:49,770 - INFO: Pre-assembling mapped reads ... 2023-02-02 12:02:52,366 - INFO: Pre-assembling mapped reads finished. 2023-02-02 12:02:52,366 - INFO: Estimated animal_mt-hitting base-coverage = 53.36 2023-02-02 12:02:52,559 - INFO: Estimated word size(s): 103 2023-02-02 12:02:52,559 - INFO: Setting '-w 103' 2023-02-02 12:02:52,559 - INFO: Setting '--max-extending-len inf' 2023-02-02 12:02:52,679 - INFO: Checking seed reads and parameters finished. 2023-02-02 12:02:52,679 - INFO: Making read index ... 2023-02-02 12:05:03,595 - INFO: 14507553 candidates in all 16618508 reads 2023-02-02 12:05:03,595 - INFO: Pre-grouping reads ... 2023-02-02 12:05:03,595 - INFO: Setting '--pre-w 103' 2023-02-02 12:05:04,965 - INFO: 200000/687070 used/duplicated 2023-02-02 12:05:33,761 - INFO: 3182 groups made. 2023-02-02 12:05:35,212 - INFO: Making read index finished. 2023-02-02 12:05:35,212 - INFO: Extending ... 2023-02-02 12:05:35,212 - INFO: Adding initial words ... 2023-02-02 12:05:35,331 - INFO: AW 104280 2023-02-02 12:11:12,814 - INFO: Round 1: 14507553/14507553 AI 2180109 AW 162579376 2023-02-02 12:12:27,258 - INFO: Round 2: 2147037/14507553 AI 2744338 AW 200187562 2023-02-02 12:12:27,258 - INFO: Hit the words limit and terminated ... 2023-02-02 12:13:28,136 - INFO: Extending finished. 2023-02-02 12:13:29,557 - INFO: Separating extended fastq file ... 2023-02-02 12:13:39,534 - INFO: Setting '-k 21,55,85,115' 2023-02-02 12:13:39,535 - INFO: Assembling using SPAdes ... 2023-02-02 12:13:39,567 - INFO: spades.py -t 8 --phred-offset 33 -1 ranita4_mt_out/extended_1_paired.fq -2 ranita4_mt_out/extended_2_paired.fq --s1 ranita4_mt_out/extended_1_unpaired.fq --s2 ranita4_mt_out/extended_2_unpaired.fq -k 21,55,85,115 -o ranita4_mt_out/extended_spades 2023-02-02 13:30:21,208 - INFO: Insert size = 278.489, deviation = 104.671, left quantile = 158, right quantile = 425 2023-02-02 13:30:21,209 - INFO: Assembling finished. 2023-02-02 13:30:21,276 - ERROR: Traceback (most recent call last): File "/home/valery/./get_organelle_from_reads.py", line 4117, in main slim_stat_list, ignore_k = slim_spades_result( File "/home/valery/./get_organelle_from_reads.py", line 3224, in slim_spades_result raise Exception("slim_graph.py not found!") Exception: slim_graph.py not found! Total cost 5454.19 s ############################## For trouble-shooting, please Firstly, check https://github.com/Kinggerm/GetOrganelle/wiki/FAQ Secondly, check if there are open/closed issues related at https://github.com/Kinggerm/GetOrganelle/issues If your problem was still not solved, please open an issue at https://github.com/Kinggerm/GetOrganelle/issues please provide the get_org.log.txt and the assembly_graph.fastg.*.fastg file(s) (can be visualized as *.png to protect your data privacy) if possible!