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 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]
PLATFORM: Linux aiken 4.15.0-126-generic #129-Ubuntu SMP Mon Nov 23 18:53:38 UTC 2020 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.25.1; sympy 1.12; scipy 1.11.1
DEPENDENCIES: Bowtie2 2.4.5; SPAdes 3.14.1; Blast 2.14.0
GETORG_PATH=/home2/rathivernir/.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: /home2/rathivernir/test
/home2/rathivernir/miniconda3/bin/get_organelle_from_reads.py -1 Arabidopsis_simulated.1.fq.gz -2 Arabidopsis_simulated.2.fq.gz -t 1 -o Arabidopsis_simulated.plastome -F embplant_pt -R 10

2023-07-20 15:07:46,443 - INFO: Pre-reading fastq ...
2023-07-20 15:07:46,443 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2023-07-20 15:07:46,706 - INFO: Estimating reads to use finished.
2023-07-20 15:07:46,707 - INFO: Unzipping reads file: Arabidopsis_simulated.1.fq.gz (8796915 bytes)
2023-07-20 15:07:49,722 - INFO: Unzipping reads file: Arabidopsis_simulated.2.fq.gz (9067061 bytes)
2023-07-20 15:07:52,763 - INFO: Counting read qualities ...
2023-07-20 15:07:53,529 - INFO: Identified quality encoding format = Illumina 1.8+
2023-07-20 15:07:53,529 - INFO: Phred offset = 33
2023-07-20 15:07:53,532 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2023-07-20 15:07:53,624 - INFO: Mean error rate = 0.0019
2023-07-20 15:07:53,625 - INFO: Counting read lengths ...
2023-07-20 15:07:58,192 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2023-07-20 15:07:58,193 - INFO: Reads used = 91563+91563
2023-07-20 15:07:58,193 - INFO: Pre-reading fastq finished.

2023-07-20 15:07:58,193 - INFO: Making seed reads ...
2023-07-20 15:07:58,199 - INFO: Seed bowtie2 index existed!
2023-07-20 15:07:58,199 - INFO: Mapping reads to seed bowtie2 index ...
2023-07-20 15:08:15,124 - INFO: Mapping finished.
2023-07-20 15:08:15,126 - INFO: Seed reads made: Arabidopsis_simulated.plastome/seed/embplant_pt.initial.fq (14144302 bytes)
2023-07-20 15:08:15,128 - INFO: Making seed reads finished.

2023-07-20 15:08:15,128 - INFO: Checking seed reads and parameters ...
2023-07-20 15:08:15,128 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-07-20 15:08:15,129 - INFO: If the result graph is not a circular organelle genome, 
2023-07-20 15:08:15,129 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2023-07-20 15:08:20,487 - INFO: Pre-assembling mapped reads ...
2023-07-20 15:08:22,996 - INFO: Retrying with more reads ..
2023-07-20 15:08:48,109 - WARNING: Pre-assembling failed. The estimations for embplant_pt-hitting base-coverage and word size may be misleading.
2023-07-20 15:08:50,748 - INFO: Estimated embplant_pt-hitting base-coverage = 52.85
2023-07-20 15:08:51,487 - INFO: Estimated word size(s): 98
2023-07-20 15:08:51,487 - INFO: Setting '-w 98'
2023-07-20 15:08:51,487 - INFO: Setting '--max-extending-len inf'
2023-07-20 15:08:51,649 - INFO: Checking seed reads and parameters finished.

2023-07-20 15:08:51,649 - INFO: Making read index ...
2023-07-20 15:08:58,578 - INFO: 178623 candidates in all 183126 reads
2023-07-20 15:08:58,579 - INFO: Pre-grouping reads ...
2023-07-20 15:08:58,579 - INFO: Setting '--pre-w 98'
2023-07-20 15:08:58,598 - INFO: 4074/4074 used/duplicated
2023-07-20 15:09:03,204 - INFO: 517 groups made.
2023-07-20 15:09:03,217 - INFO: Making read index finished.

2023-07-20 15:09:03,218 - INFO: Extending ...
2023-07-20 15:09:03,218 - INFO: Adding initial words ...
2023-07-20 15:09:05,171 - INFO: AW 1113742
2023-07-20 15:09:07,234 - INFO: Round 1: 178623/178623 AI 40378 AW 1126044
2023-07-20 15:09:08,244 - INFO: Round 2: 178623/178623 AI 40411 AW 1126346
2023-07-20 15:09:09,254 - INFO: Round 3: 178623/178623 AI 40411 AW 1126346
2023-07-20 15:09:09,255 - INFO: No more reads found and terminated ...
2023-07-20 15:09:11,311 - INFO: Extending finished.

2023-07-20 15:09:11,339 - INFO: Separating extended fastq file ... 
2023-07-20 15:09:14,234 - INFO: Setting '-k 21,55,85,115'
2023-07-20 15:09:14,234 - INFO: Assembling using SPAdes ...
2023-07-20 15:09:14,277 - INFO: spades.py -t 1  --phred-offset 33 -1 Arabidopsis_simulated.plastome/extended_1_paired.fq -2 Arabidopsis_simulated.plastome/extended_2_paired.fq --s1 Arabidopsis_simulated.plastome/extended_1_unpaired.fq --s2 Arabidopsis_simulated.plastome/extended_2_unpaired.fq -k 21,55,85,115 -o Arabidopsis_simulated.plastome/extended_spades
2023-07-20 15:09:15,108 - WARNING: Assembling exited halfway.

2023-07-20 15:09:15,764 - ERROR: No valid assembly graph found!
2023-07-20 15:09:15,764 - WARNING: This might due to a damaged dependency, to unreasonable seed/parameter choices, or to a bug.
2023-07-20 15:09:15,764 - INFO: Please first search similar issues at https://github.com/Kinggerm/GetOrganelle/issues, then leave your message following the same issue, or open an issue at https://github.com/Kinggerm/GetOrganelle/issues if it is new, Please always attach the get_org.log.txt file.


Total cost 94.49 s
Thank you!