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 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0] PLATFORM: Linux dongfei 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UTC 2023 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.21.6; sympy 1.10.1; scipy 1.7.3 DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.5.0 GETORG_PATH=/software/GetOrganelle/GetOrganelleLib SEED DB: embplant_mt customized; embplant_pt customized LABEL DB: embplant_mt customized; embplant_pt customized WORKING DIR: /data2/wangyan_backup/xhx/53/3/1 /home/kongss/anaconda3/envs/getorganelle/bin/get_organelle_from_reads.py -1 /mnt/nas1/Original_Sequences_data_2024/XHX/30GNew/53/X49/X49/X49-01_R1.fq -2 /mnt/nas1/Original_Sequences_data_2024/XHX/30GNew/53/X49/X49/X49-01_R2.fq -o mitochondria_output -R 20 -k 21,45,65,85,105 -P 1000000 -F embplant_mt 2024-11-21 18:54:45,767 - INFO: Pre-reading fastq ... 2024-11-21 18:54:45,768 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf') 2024-11-21 18:54:45,879 - INFO: Tasting 100000+100000 reads ... 2024-11-21 18:54:59,294 - INFO: Tasting 500000+500000 reads ... 2024-11-21 18:55:20,039 - INFO: Tasting 2500000+2500000 reads ... 2024-11-21 18:56:55,853 - INFO: Estimating reads to use finished. 2024-11-21 18:59:50,828 - INFO: Counting read qualities ... 2024-11-21 18:59:51,070 - INFO: Identified quality encoding format = Sanger 2024-11-21 18:59:51,070 - INFO: Phred offset = 33 2024-11-21 18:59:51,071 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2024-11-21 18:59:51,138 - INFO: Mean error rate = 0.0011 2024-11-21 18:59:51,139 - INFO: Counting read lengths ... 2024-11-21 19:00:52,388 - INFO: Mean = 150.0 bp, maximum = 150 bp. 2024-11-21 19:00:52,388 - INFO: Reads used = 27881379+27881379 2024-11-21 19:00:52,388 - INFO: Pre-reading fastq finished. 2024-11-21 19:00:52,388 - INFO: Making seed reads ... 2024-11-21 19:00:52,528 - INFO: Making seed - bowtie2 index ... 2024-11-21 19:00:53,417 - INFO: Making seed - bowtie2 index finished. 2024-11-21 19:00:53,418 - INFO: Mapping reads to seed bowtie2 index ... 2024-11-21 19:11:10,581 - INFO: Mapping finished. 2024-11-21 19:11:10,582 - INFO: Seed reads made: mitochondria_output/seed/embplant_mt.initial.fq (19074384 bytes) 2024-11-21 19:11:10,583 - INFO: Making seed reads finished. 2024-11-21 19:11:10,583 - INFO: Checking seed reads and parameters ... 2024-11-21 19:11:10,583 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s). 2024-11-21 19:11:10,583 - INFO: If the result graph is not a circular organelle genome, 2024-11-21 19:11:10,583 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run. 2024-11-21 19:11:22,226 - INFO: Pre-assembling mapped reads ... 2024-11-21 19:11:50,294 - INFO: Pre-assembling mapped reads finished. 2024-11-21 19:11:50,294 - INFO: Estimated embplant_mt-hitting base-coverage = 143.68 2024-11-21 19:11:53,584 - INFO: Estimated word size(s): 98 2024-11-21 19:11:53,584 - INFO: Setting '-w 98' 2024-11-21 19:11:53,584 - INFO: Setting '--max-extending-len inf' 2024-11-21 19:11:53,715 - INFO: Checking seed reads and parameters finished. 2024-11-21 19:11:53,715 - INFO: Making read index ... 2024-11-21 19:18:37,975 - INFO: 54599539 candidates in all 55762758 reads 2024-11-21 19:18:37,987 - INFO: Pre-grouping reads ... 2024-11-21 19:18:37,987 - INFO: Setting '--pre-w 98' 2024-11-21 19:18:43,112 - INFO: 780899/780899 used/duplicated 2024-11-21 19:21:56,236 - INFO: 12850 groups made. 2024-11-21 19:22:08,922 - INFO: Making read index finished. 2024-11-21 19:22:08,923 - INFO: Extending ... 2024-11-21 19:22:08,923 - INFO: Adding initial words ... 2024-11-21 19:22:10,571 - INFO: AW 579370 2024-11-21 19:28:23,544 - INFO: Round 1: 54599539/54599539 AI 578245 AW 2837734 2024-11-21 19:34:26,587 - INFO: Round 2: 54599539/54599539 AI 1130617 AW 9972212 2024-11-21 19:41:19,009 - INFO: Round 3: 54599539/54599539 AI 3453836 AW 54819679 2024-11-21 19:50:51,610 - INFO: Round 4: 54599539/54599539 AI 7520072 AW 135733230 2024-11-21 19:58:49,559 - INFO: Round 5: 54599539/54599539 AI 10596682 AW 203739081 2024-11-21 20:05:07,127 - INFO: Round 6: 54599539/54599539 AI 12538910 AW 250625336 2024-11-21 20:11:02,101 - INFO: Round 7: 54599539/54599539 AI 13645344 AW 280778532 2024-11-21 20:16:57,089 - INFO: Round 8: 54599539/54599539 AI 14361091 AW 300951880 2024-11-21 20:22:37,917 - INFO: Round 9: 54599539/54599539 AI 14917369 AW 316442750 2024-11-21 20:30:56,393 - INFO: Round 10: 54599539/54599539 AI 15373701 AW 328851722 2024-11-21 20:38:36,150 - INFO: Round 11: 54599539/54599539 AI 15675097 AW 337488234 2024-11-21 20:44:14,724 - INFO: Round 12: 54599539/54599539 AI 15899752 AW 343923014 2024-11-21 20:49:33,985 - INFO: Round 13: 54599539/54599539 AI 16077685 AW 348989998 2024-11-21 20:54:48,367 - INFO: Round 14: 54599539/54599539 AI 16217452 AW 352973658 2024-11-21 20:59:54,735 - INFO: Round 15: 54599539/54599539 AI 16326578 AW 356134116 2024-11-21 21:05:06,221 - INFO: Round 16: 54599539/54599539 AI 16413984 AW 358660682 2024-11-21 21:10:22,498 - INFO: Round 17: 54599539/54599539 AI 16482890 AW 360645442 2024-11-21 21:15:31,051 - INFO: Round 18: 54599539/54599539 AI 16539498 AW 362289358 2024-11-21 21:20:35,717 - INFO: Round 19: 54599539/54599539 AI 16588168 AW 363698020 2024-11-21 21:25:42,906 - INFO: Round 20: 54599539/54599539 AI 16629574 AW 364888416 2024-11-21 21:25:42,907 - INFO: Hit the round limit 20 and terminated ... 2024-11-21 23:38:17,471 - INFO: Extending finished. 2024-11-21 23:38:20,973 - INFO: Separating extended fastq file ... 2024-11-21 23:39:11,584 - INFO: Setting '-k 21,45,65,85,105' 2024-11-21 23:39:11,585 - INFO: Assembling using SPAdes ... 2024-11-21 23:39:12,281 - INFO: spades.py -t 1 --phred-offset 33 -1 mitochondria_output/extended_1_paired.fq -2 mitochondria_output/extended_2_paired.fq --s1 mitochondria_output/extended_1_unpaired.fq --s2 mitochondria_output/extended_2_unpaired.fq -k 21,45,65,85,105 -o mitochondria_output/extended_spades 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 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0] PLATFORM: Linux dongfei 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UTC 2023 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.21.6; sympy 1.10.1; scipy 1.7.3 DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.5.0 GETORG_PATH=/software/GetOrganelle/GetOrganelleLib SEED DB: embplant_mt customized; embplant_pt customized LABEL DB: embplant_mt customized; embplant_pt customized WORKING DIR: /data2/wangyan_backup/xhx/53/3/1 /home/kongss/anaconda3/envs/getorganelle/bin/get_organelle_from_reads.py -1 /mnt/nas1/Original_Sequences_data_2024/XHX/30GNew/53/X49/X49/X49-01_R1.fq -2 /mnt/nas1/Original_Sequences_data_2024/XHX/30GNew/53/X49/X49/X49-01_R2.fq -o mitochondria_output -R 20 -k 21,45,65,85,105 -P 1000000 -F embplant_mt --continue 2024-11-22 09:31:44,515 - INFO: Extending ... skipped. 2024-11-22 09:31:44,516 - INFO: Separating extended fastq file ... skipped. 2024-11-22 09:31:44,516 - INFO: Setting '-k 21,45,65,85,105' 2024-11-22 09:31:44,516 - INFO: Assembling using SPAdes ... 2024-11-22 09:31:44,547 - INFO: spades.py --continue -o mitochondria_output/extended_spades 2024-11-22 11:32:45,172 - ERROR: Error with running SPAdes: == Error == system call for: "['/home/kongss/anaconda3/envs/getorganelle/share/spades-3.13.0-0/bin/spades-core', '/data2/wangyan_backup/xhx/53/3/1/mitochondria_output/extended_spades/K105/configs/config.info']" finished abnormally, err code: 255 2024-11-22 11:32:45,386 - ERROR: Error with running SPAdes: == Error == exception caught: 2024-11-22 11:32:45,753 - WARNING: SPAdes failed for '-k 105'! 2024-11-22 11:32:45,753 - WARNING: If you need result based on kmer=105 urgently, please check mitochondria_output/extended_spades/spades.log 2024-11-22 11:32:45,753 - WARNING: GetOrganelle would continue to process results based on kmer=21,45,65,85. 2024-11-22 11:32:45,753 - INFO: Assembling finished with warnings. 2024-11-22 11:35:09,828 - INFO: Slimming mitochondria_output/extended_spades/K85/assembly_graph.fastg finished! 2024-11-22 11:41:57,676 - INFO: Slimming mitochondria_output/extended_spades/K65/assembly_graph.fastg finished! 2024-11-23 11:29:31,283 - INFO: Slimming mitochondria_output/extended_spades/K45/assembly_graph.fastg finished! 2024-11-23 11:29:31,339 - INFO: Slimming assembly graphs finished. 2024-11-23 11:29:31,368 - INFO: Extracting embplant_mt from the assemblies ... 2024-11-23 11:29:31,641 - INFO: Disentangling mitochondria_output/extended_spades/K85/assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg as a circular genome ... 2024-11-23 11:38:46,328 - INFO: Disentangling failed: 'Multiple isolated embplant_mt components detected! Broken or contamination?' 2024-11-23 11:38:46,460 - INFO: Disentangling mitochondria_output/extended_spades/K65/assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg as a circular genome ... 2024-11-23 11:56:11,041 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_120904463!' 2024-11-23 11:56:11,225 - INFO: Disentangling mitochondria_output/extended_spades/K45/assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg as a circular genome ... 2024-11-23 12:26:11,226 - INFO: Disentangling timeout. (see '--disentangle-time-limit' for more) 2024-11-23 12:26:14,922 - ERROR: Traceback (most recent call last): File "/home/kongss/anaconda3/envs/getorganelle/bin/get_organelle_from_reads.py", line 4170, in main do_spades_scaffolding=reads_paired["input"]) File "/home/kongss/anaconda3/envs/getorganelle/bin/get_organelle_from_reads.py", line 3589, in extract_organelle_genome out_fastg = slim_out_fg[go_k] IndexError: list index out of range Total cost 96871.77 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!