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 gs133 4.15.0-206-generic #217-Ubuntu SMP Fri Feb 3 19:10:13 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; Bandage 0.8.1
GETORG_PATH=/home/ug1602/.GetOrganelle
LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1
WORKING DIR: /home/ug1602
/home/ug1602/.conda/envs/getorganelle/bin/get_organelle_from_reads.py -1 /home/ug1602/data/M10-1_clean_1.fq.gz -2 /home/ug1602/data/M10-1_clean_2.fq.gz --max-reads inf -o plastome_output --overwrite -R 10 -k 21,71,121 -F embplant_pt -s /home/ug1602/data/cp_reference.fas -t 10

2023-12-04 22:19:59,756 - INFO: Pre-reading fastq ...
2023-12-04 22:19:59,756 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2023-12-04 22:19:59,846 - INFO: Tasting 100000+100000 reads ...
2023-12-04 22:20:06,689 - INFO: Tasting 500000+500000 reads ...
2023-12-04 22:20:23,001 - INFO: Estimating reads to use finished.
2023-12-04 22:20:23,001 - INFO: Unzipping reads file: /home/ug1602/data/M10-1_clean_1.fq.gz (9670687718 bytes)
2023-12-04 22:22:04,428 - INFO: Unzipping reads file: /home/ug1602/data/M10-1_clean_2.fq.gz (10713058869 bytes)
2023-12-04 22:23:40,315 - INFO: Counting read qualities ...
2023-12-04 22:23:40,568 - INFO: Identified quality encoding format = Sanger
2023-12-04 22:23:40,568 - INFO: Phred offset = 33
2023-12-04 22:23:40,569 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2023-12-04 22:23:40,678 - INFO: Mean error rate = 0.0052
2023-12-04 22:23:40,680 - INFO: Counting read lengths ...
2023-12-04 22:24:49,058 - INFO: Mean = 149.2 bp, maximum = 150 bp.
2023-12-04 22:24:49,058 - INFO: Reads used = 25464063+25464063
2023-12-04 22:24:49,058 - INFO: Pre-reading fastq finished.

2023-12-04 22:24:49,059 - INFO: Making seed reads ...
2023-12-04 22:24:49,078 - INFO: Making seed - bowtie2 index ...
2023-12-04 22:24:50,226 - INFO: Making seed - bowtie2 index finished.
2023-12-04 22:24:50,227 - INFO: Mapping reads to seed bowtie2 index ...
2023-12-04 22:30:44,265 - INFO: Mapping finished.
2023-12-04 22:30:44,266 - INFO: Seed reads made: plastome_output/seed/embplant_pt.initial.fq (302290511 bytes)
2023-12-04 22:30:44,266 - INFO: Making seed reads finished.

2023-12-04 22:30:44,266 - INFO: Checking seed reads and parameters ...
2023-12-04 22:30:44,266 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-12-04 22:30:44,267 - INFO: If the result graph is not a circular organelle genome, 
2023-12-04 22:30:44,267 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2023-12-04 22:32:04,381 - INFO: Pre-assembling mapped reads ...
2023-12-04 22:32:39,121 - ERROR: slimming the pre-assembled graph failed.
2023-12-04 22:32:39,137 - INFO: Pre-assembling mapped reads finished.
2023-12-04 22:32:39,137 - INFO: Estimated embplant_pt-hitting base-coverage = 790.23
2023-12-04 22:32:39,701 - INFO: Reads reduced to = 16111863+16111863
2023-12-04 22:32:39,702 - INFO: Adjusting expected embplant_pt base coverage to 500.00
2023-12-04 22:32:39,703 - INFO: Estimated word size(s): 111
2023-12-04 22:32:39,703 - INFO: Setting '-w 111'
2023-12-04 22:32:39,703 - INFO: Setting '--max-extending-len inf'
2023-12-04 22:32:42,613 - INFO: Checking seed reads and parameters finished.

2023-12-04 22:32:42,614 - INFO: Making read index ...
2023-12-04 22:35:23,521 - INFO: For plastome_output/1-M10-1_clean_1.fq.gz.fastq, only top 16111863 reads are used in downstream analysis.
2023-12-04 22:38:32,340 - INFO: For plastome_output/2-M10-1_clean_2.fq.gz.fastq, only top 16111863 reads are used in downstream analysis.
2023-12-04 22:38:59,808 - INFO: 31497665 candidates in all 32223726 reads
2023-12-04 22:38:59,809 - INFO: Pre-grouping reads ...
2023-12-04 22:38:59,809 - INFO: Setting '--pre-w 111'
2023-12-04 22:39:05,106 - INFO: 200000/313663 used/duplicated
2023-12-04 22:39:39,621 - INFO: 5014 groups made.
2023-12-04 22:39:52,226 - INFO: Making read index finished.

2023-12-04 22:39:52,226 - INFO: Extending ...
2023-12-04 22:39:52,226 - INFO: Adding initial words ...
2023-12-04 22:40:28,253 - INFO: AW 9086654
2023-12-04 22:45:10,922 - INFO: Round 1: 31497665/31497665 AI 376887 AW 9117304
2023-12-04 22:49:36,812 - INFO: Round 2: 31497665/31497665 AI 379672 AW 9133354
2023-12-04 22:53:07,723 - INFO: Round 3: 31497665/31497665 AI 384080 AW 9154852
2023-12-04 22:56:08,246 - INFO: Round 4: 31497665/31497665 AI 386545 AW 9167218
2023-12-04 22:59:08,657 - INFO: Round 5: 31497665/31497665 AI 388982 AW 9180284
2023-12-04 23:02:10,527 - INFO: Round 6: 31497665/31497665 AI 392097 AW 9197976
2023-12-04 23:05:15,173 - INFO: Round 7: 31497665/31497665 AI 395272 AW 9214474
2023-12-04 23:08:18,870 - INFO: Round 8: 31497665/31497665 AI 398021 AW 9229130
2023-12-04 23:11:24,883 - INFO: Round 9: 31497665/31497665 AI 401055 AW 9245284
2023-12-04 23:14:28,076 - INFO: Round 10: 31497665/31497665 AI 404254 AW 9262238
2023-12-04 23:14:28,076 - INFO: Hit the round limit 10 and terminated ...
2023-12-04 23:15:18,862 - INFO: Extending finished.

2023-12-04 23:15:21,898 - INFO: Separating extended fastq file ... 
2023-12-04 23:15:23,748 - INFO: Setting '-k 21,71,121'
2023-12-04 23:15:23,748 - INFO: Assembling using SPAdes ...
2023-12-04 23:15:23,771 - INFO: spades.py -t 10  --phred-offset 33 -1 plastome_output/extended_1_paired.fq -2 plastome_output/extended_2_paired.fq --s1 plastome_output/extended_1_unpaired.fq --s2 plastome_output/extended_2_unpaired.fq -k 21,71,121 -o plastome_output/extended_spades
2023-12-04 23:16:33,884 - INFO: Insert size = 385.994, deviation = 101.552, left quantile = 240, right quantile = 508
2023-12-04 23:16:33,885 - INFO: Assembling finished.

2023-12-04 23:16:35,316 - ERROR: Slimming plastome_output/extended_spades/K121/assembly_graph.fastg failed. Please check plastome_output/extended_spades/K121/slim.log.txt for details. 
2023-12-04 23:16:36,383 - ERROR: Slimming plastome_output/extended_spades/K71/assembly_graph.fastg failed. Please check plastome_output/extended_spades/K71/slim.log.txt for details. 
2023-12-04 23:16:36,384 - ERROR: No valid assembly graph found!
2023-12-04 23:16:36,384 - WARNING: This might due to a damaged dependency, to unreasonable seed/parameter choices, or to a bug.
2023-12-04 23:16:36,384 - 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 3398.35 s
Thank you!