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GetOrganelle v1.6.3a
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 3.9.1 | packaged by conda-forge | (default, Dec 9 2020, 01:12:47) [GCC 9.3.0]
Python libs: numpy 1.20.2; scipy 1.6.3
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
/data1/guop/software/GetOrganelle/get_organelle_from_reads.py -1 14-1_1.clean.fq.gz -2 14-1_2.clean.fq.gz -o chloroplast_output -R 15 -k 45,65,85,105 -F embplant_pt
2022-05-14 18:52:42,771 - INFO: Pre-reading fastq ...
2022-05-14 18:52:42,771 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2022-05-14 18:52:43,480 - INFO: Tasting 100000+100000 reads ...
2022-05-14 18:52:58,742 - INFO: Estimating reads to use finished.
2022-05-14 18:52:58,743 - INFO: Unzipping reads file: 14-1_1.clean.fq.gz (2599004268 bytes)
2022-05-14 18:53:25,991 - INFO: Unzipping reads file: 14-1_2.clean.fq.gz (2700381284 bytes)
2022-05-14 18:53:53,332 - INFO: Counting read qualities ...
2022-05-14 18:53:53,535 - INFO: Identified quality encoding format = Sanger
2022-05-14 18:53:53,538 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2022-05-14 18:53:53,601 - INFO: Mean error rate = 0.003
2022-05-14 18:53:53,603 - INFO: Counting read lengths ...
2022-05-14 18:54:23,153 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2022-05-14 18:54:23,153 - INFO: Reads used = 8056086+8056086
2022-05-14 18:54:23,153 - INFO: Pre-reading fastq finished.
2022-05-14 18:54:23,153 - INFO: Making seed reads ...
2022-05-14 18:54:23,169 - INFO: Making seed - bowtie2 index ...
2022-05-14 18:54:23,657 - INFO: Making seed - bowtie2 index finished.
2022-05-14 18:54:23,657 - INFO: Mapping reads to seed bowtie2 index ...
2022-05-14 19:01:57,505 - INFO: Mapping finished.
2022-05-14 19:01:57,506 - INFO: Seed reads made: chloroplast_output/seed/embplant_pt.initial.fq (212962960 bytes)
2022-05-14 19:01:57,507 - INFO: Making seed reads finished.
2022-05-14 19:01:57,507 - INFO: Checking seed reads and parameters ...
2022-05-14 19:01:57,507 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2022-05-14 19:01:57,507 - INFO: If the result graph is not a circular organelle genome,
2022-05-14 19:01:57,507 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2022-05-14 19:02:38,822 - INFO: Pre-assembling mapped reads ...
2022-05-14 19:04:07,526 - INFO: Pre-assembling mapped reads finished.
2022-05-14 19:04:07,527 - INFO: Estimated embplant_pt-hitting base-coverage = 824.49
2022-05-14 19:04:07,527 - INFO: Reads reduced to = 4885475+4885475
2022-05-14 19:04:07,527 - INFO: Adjusting expected embplant_pt base coverage to 500.00
2022-05-14 19:04:07,527 - INFO: Estimated word size(s): 112
2022-05-14 19:04:07,528 - INFO: Setting '-w 112'
2022-05-14 19:04:07,528 - INFO: Setting '--max-extending-len inf'
2022-05-14 19:04:09,255 - INFO: Checking seed reads and parameters finished.
2022-05-14 19:04:09,256 - INFO: Making read index ...
2022-05-14 19:04:56,105 - INFO: For chloroplast_output/1-14-1_1.clean.fq.gz.fastq, only top 4885475 reads are used in downstream analysis.
2022-05-14 19:05:45,243 - INFO: For chloroplast_output/2-14-1_2.clean.fq.gz.fastq, only top 4885475 reads are used in downstream analysis.
2022-05-14 19:05:56,334 - INFO: 8195598 candidates in all 9770950 reads
2022-05-14 19:05:56,404 - INFO: Pre-grouping reads ...
2022-05-14 19:05:56,404 - INFO: Setting '--pre-w 112'
2022-05-14 19:05:58,028 - INFO: 200000/1114284 used/duplicated
2022-05-14 19:06:29,120 - INFO: 3046 groups made.
2022-05-14 19:06:31,238 - INFO: Making read index finished.
2022-05-14 19:06:31,239 - INFO: Extending ...
2022-05-14 19:06:31,239 - INFO: Adding initial words ...
2022-05-14 19:06:57,897 - INFO: AW 4769882
2022-05-14 19:08:15,450 - INFO: Round 1: 8195598/8195598 AI 193610 AW 5261682
2022-05-14 19:09:23,546 - INFO: Round 2: 8195598/8195598 AI 195480 AW 5296622
2022-05-14 19:10:31,274 - INFO: Round 3: 8195598/8195598 AI 195522 AW 5297914
2022-05-14 19:11:39,577 - INFO: Round 4: 8195598/8195598 AI 195524 AW 5297976
2022-05-14 19:12:48,443 - INFO: Round 5: 8195598/8195598 AI 195524 AW 5297976
2022-05-14 19:12:48,444 - INFO: No more reads found and terminated ...
2022-05-14 19:13:11,989 - INFO: Extending finished.
2022-05-14 19:13:13,540 - INFO: Separating filtered fastq file ...
2022-05-14 19:13:15,848 - INFO: Setting '-k 45,65,85,105'
2022-05-14 19:13:15,849 - INFO: Assembling using SPAdes ...
2022-05-14 19:21:14,040 - INFO: Insert size = 393.892, deviation = 79.3577, left quantile = 294, right quantile = 494
2022-05-14 19:21:14,040 - INFO: Assembling finished.
2022-05-14 19:21:14,040 - INFO: Slimming assembly graphs ...
2022-05-14 19:21:15,521 - INFO: Slimming chloroplast_output/filtered_spades/K105/assembly_graph.fastg finished!
2022-05-14 19:21:16,992 - INFO: Slimming chloroplast_output/filtered_spades/K85/assembly_graph.fastg finished!
2022-05-14 19:21:18,714 - INFO: Slimming chloroplast_output/filtered_spades/K65/assembly_graph.fastg finished!
2022-05-14 19:21:20,325 - INFO: Slimming chloroplast_output/filtered_spades/K45/assembly_graph.fastg finished!
2022-05-14 19:21:20,326 - INFO: Slimming assembly graphs finished.
2022-05-14 19:21:20,326 - INFO: Extracting embplant_pt from the assemblies ...
2022-05-14 19:21:20,327 - INFO: Disentangling chloroplast_output/filtered_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-05-14 19:21:20,346 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_85410!'
2022-05-14 19:21:20,347 - INFO: Disentangling chloroplast_output/filtered_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-05-14 19:21:20,361 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_90406!'
2022-05-14 19:21:20,361 - INFO: Disentangling chloroplast_output/filtered_spades/K65/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-05-14 19:21:20,373 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_94458!'
2022-05-14 19:21:20,374 - INFO: Disentangling chloroplast_output/filtered_spades/K45/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2022-05-14 19:21:20,385 - INFO: Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_27316!'
2022-05-14 19:21:20,386 - INFO: Disentangling chloroplast_output/filtered_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as contig(s) ...
2022-05-14 19:21:20,396 - INFO: Please ...
2022-05-14 19:21:20,397 - INFO: load the graph file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg,assembly_graph.fastg' in K105,K85,K65,K45
2022-05-14 19:21:20,397 - INFO: load the CSV file 'assembly_graph.fastg.extend-embplant_pt-embplant_mt.csv' in K105,K85,K65,K45
2022-05-14 19:21:20,397 - INFO: visualize and export your result in Bandage.
2022-05-14 19:21:20,397 - INFO: If you have questions for us, please provide us with the get_org.log.txt file and the graph in the format you like!
2022-05-14 19:21:20,397 - INFO: Extracting embplant_pt from the assemblies failed.
Total cost 1718.27 s
Thank you!
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