Too many results due to palindromic repeats #25
Comments
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Hi @Li-Rui091 This is an interesting and exciting result! Thanks for the log file and Bandage image, very helpful. Best, |
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Hi, @Kinggerm, |
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Hi @Li-Rui091 |
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Hi, @Kinggerm, |
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If sequences are completely identical, it should be the problem of the annotation tool. I think your assembly issue is solved and I close this issue. Feel free to open it if you have more questions on assembly. |
Kinggerm
changed the title
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I have updated GetOrganelle to 1.6.3, which will recognize the palindromic repeats and suppress a large amount of redundant repeated paths. |
Hi, @Kinggerm,
I am trying to use GetOrganelle to assemble the chloroplast of my plant. In the process，I got 512 results. However,I don’t know how to choose the best one.
Here is the full log:
GetOrganelle v1.6.2
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 2.7.5 (default, Jul 13 2018, 13:06:57) [GCC 4.8.5 20150623 (Red Hat 4.8.5-28)]
Python libs: numpy 1.15.2; sympy 1.4; scipy 1.2.2
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
/tmp/user249/GetOrganelle-master/get_organelle_from_reads.py -1 Nitella-fuiana_FDSW190040255-1a_1.clean.fq.gz -2 Nitella-fuiana_FDSW190040255-1a_2.clean.fq.gz -o plastome_output2 -R 15 -k 21,45,65,85,105 -F embplant_pt
2019-06-27 16:41:58,344 - INFO: Pre-reading fastq ...
2019-06-27 16:41:58,345 - INFO: Estimating reads to use ...
2019-06-27 16:41:59,763 - INFO: Tasting 100000+100000 reads ...
2019-06-27 16:42:14,178 - INFO: Estimating reads to use finished.
2019-06-27 16:42:14,180 - INFO: Unzipping reads file: Nitella-fuiana_FDSW190040255-1a_1.clean.fq.gz (1737988090 bytes)
2019-06-27 16:42:39,201 - INFO: Unzipping reads file: Nitella-fuiana_FDSW190040255-1a_2.clean.fq.gz (1856381193 bytes)
2019-06-27 16:43:04,840 - INFO: Counting read qualities ...
2019-06-27 16:43:05,063 - INFO: Identified quality encoding format = Illumina 1.8+
2019-06-27 16:43:05,067 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2019-06-27 16:43:05,162 - INFO: Mean error rate = 0.0034
2019-06-27 16:43:05,165 - INFO: Counting read lengths ...
2019-06-27 16:43:46,480 - INFO: Mean = 149.0 bp, maximum = 150 bp.
2019-06-27 16:43:46,482 - INFO: Reads used = 9209044+9209044
2019-06-27 16:43:46,482 - INFO: Pre-reading fastq finished.
2019-06-27 16:43:46,483 - INFO: Making seed reads ...
2019-06-27 16:43:46,486 - INFO: Seed bowtie2 index existed!
2019-06-27 16:43:46,486 - INFO: Mapping reads to seed bowtie2 index ...
2019-06-27 16:53:13,473 - INFO: Mapping finished.
2019-06-27 16:53:13,474 - INFO: Seed reads made: plastome_output2/seed/embplant_pt.initial.fq (13948724 bytes)
2019-06-27 16:53:13,475 - INFO: Making seed reads finished.
2019-06-27 16:53:13,476 - INFO: Checking seed reads and parameters ...
2019-06-27 16:53:13,476 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2019-06-27 16:53:13,477 - INFO: If the result graph is not a circular organelle genome,
2019-06-27 16:53:13,477 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2019-06-27 16:53:20,015 - INFO: Pre-assembling mapped reads ...
2019-06-27 16:53:34,726 - INFO: Pre-assembling mapped reads finished.
2019-06-27 16:53:34,727 - INFO: Estimated embplant_pt-hitting base-coverage = 1182.87
2019-06-27 16:53:34,728 - INFO: Reads reduced to = 3892673+3892673
2019-06-27 16:53:34,728 - INFO: Adjusting expected embplant_pt base coverage to 500.00
2019-06-27 16:53:34,729 - INFO: Estimated word size(s): 111
2019-06-27 16:53:34,729 - INFO: Setting '-w 111'
2019-06-27 16:53:34,730 - INFO: Setting '--max-extending-len inf'
2019-06-27 16:53:34,974 - INFO: Checking seed reads and parameters finished.
2019-06-27 16:53:34,976 - INFO: Making read index ...
2019-06-27 16:54:35,825 - INFO: For plastome_output2/1-Nitella-fuiana_FDSW190040255-1a_1.clean.fq.gz.fastq, only top 3892673 reads are used in downstream analysis.
2019-06-27 16:55:36,381 - INFO: For plastome_output2/2-Nitella-fuiana_FDSW190040255-1a_2.clean.fq.gz.fastq, only top 3892673 reads are used in downstream analysis.
2019-06-27 16:55:46,930 - INFO: 6417111 candidates in all 7785346 reads
2019-06-27 16:55:46,956 - INFO: Pre-grouping reads ...
2019-06-27 16:55:46,957 - INFO: Setting '--pre-w 111'
2019-06-27 16:55:49,867 - INFO: 200000/1000496 used/duplicated
2019-06-27 16:56:15,625 - INFO: 1061 groups made.
2019-06-27 16:56:16,949 - INFO: Making read index finished.
2019-06-27 16:56:17,116 - INFO: Extending ...
2019-06-27 16:56:17,120 - INFO: Adding initial words ...
2019-06-27 16:56:18,680 - INFO: AW 256854
2019-06-27 16:57:21,367 - INFO: Round 1: 6417111/6417111 AI 116029 AW 805462
2019-06-27 16:58:25,368 - INFO: Round 2: 6417111/6417111 AI 156185 AW 989754
2019-06-27 16:59:28,833 - INFO: Round 3: 6417111/6417111 AI 170285 AW 1058468
2019-06-27 17:00:32,138 - INFO: Round 4: 6417111/6417111 AI 172792 AW 1070134
2019-06-27 17:01:35,321 - INFO: Round 5: 6417111/6417111 AI 172830 AW 1070508
2019-06-27 17:02:38,258 - INFO: Round 6: 6417111/6417111 AI 172839 AW 1070750
2019-06-27 17:03:41,602 - INFO: Round 7: 6417111/6417111 AI 172846 AW 1070920
2019-06-27 17:04:45,846 - INFO: Round 8: 6417111/6417111 AI 172853 AW 1071032
2019-06-27 17:05:49,208 - INFO: Round 9: 6417111/6417111 AI 172854 AW 1071072
2019-06-27 17:06:54,784 - INFO: Round 10: 6417111/6417111 AI 172854 AW 1071072
2019-06-27 17:06:54,786 - INFO: No more reads found and terminated ...
2019-06-27 17:07:27,185 - INFO: Extending finished.
2019-06-27 17:07:27,187 - INFO: Separating filtered fastq file ...
2019-06-27 17:07:29,817 - INFO: Setting '-k 21,45,65,85,105'
2019-06-27 17:07:29,818 - INFO: Assembling using SPAdes ...
2019-06-27 17:12:24,214 - INFO: Insert size = 370.581, deviation = 74.658, left quantile = 277, right quantile = 465
2019-06-27 17:12:24,215 - INFO: Assembling finished.
2019-06-27 17:12:24,216 - INFO: Slimming assembly graphs ...
2019-06-27 17:12:26,244 - INFO: Slimming plastome_output2/filtered_spades/K105/assembly_graph.fastg finished!
2019-06-27 17:12:28,206 - INFO: Slimming plastome_output2/filtered_spades/K85/assembly_graph.fastg finished!
2019-06-27 17:12:30,174 - INFO: Slimming plastome_output2/filtered_spades/K65/assembly_graph.fastg finished!
2019-06-27 17:12:32,142 - INFO: Slimming plastome_output2/filtered_spades/K45/assembly_graph.fastg finished!
2019-06-27 17:12:32,143 - INFO: Slimming assembly graphs finished
2019-06-27 17:12:32,144 - INFO: Extracting embplant_pt from the assemblies ...
2019-06-27 17:12:32,149 - INFO: Disentangling plastome_output2/filtered_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2019-06-27 17:22:32,150 - INFO: Disentangling timeout. (see '--disentangle-time-limit' for more)
2019-06-27 17:22:32,152 - INFO: Disentangling plastome_output2/filtered_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2019-06-27 17:25:18,777 - INFO: Vertex_2654 #copy = 1
2019-06-27 17:25:18,778 - INFO: Vertex_32157 #copy = 1
2019-06-27 17:25:18,779 - INFO: Vertex_32228 #copy = 1
2019-06-27 17:25:18,780 - INFO: Vertex_33112 #copy = 1
2019-06-27 17:25:18,780 - INFO: Vertex_35113 #copy = 1
2019-06-27 17:25:18,781 - INFO: Vertex_35677 #copy = 1
2019-06-27 17:25:18,781 - INFO: Vertex_35783 #copy = 1
2019-06-27 17:25:18,782 - INFO: Vertex_35851 #copy = 1
2019-06-27 17:25:18,783 - INFO: Vertex_35897 #copy = 1
2019-06-27 17:25:18,783 - INFO: Vertex_35903 #copy = 1
2019-06-27 17:25:18,784 - INFO: Vertex_35939 #copy = 1
2019-06-27 17:25:18,785 - INFO: Vertex_35951 #copy = 1
2019-06-27 17:25:18,785 - INFO: Vertex_35957 #copy = 1
2019-06-27 17:25:18,786 - INFO: Vertex_35963 #copy = 2
2019-06-27 17:25:18,787 - INFO: Vertex_35969 #copy = 2
2019-06-27 17:25:18,787 - INFO: Vertex_5158 #copy = 2
2019-06-27 17:25:18,788 - INFO: Vertex_5244 #copy = 1
2019-06-27 17:25:18,788 - INFO: Vertex_5590 #copy = 1
2019-06-27 17:25:18,789 - INFO: Vertex_8058 #copy = 1
2019-06-27 17:25:18,789 - INFO: Average embplant_pt kmer-coverage = 150.721
2019-06-27 17:25:18,789 - INFO: Average embplant_pt base-coverage = 345.499
2019-06-27 17:25:18,790 - INFO: Writing output ...
2019-06-27 17:25:19,493 - WARNING: Multiple circular genome structures produced!
2019-06-27 17:25:19,494 - WARNING: Please check the existence of those isomers by using reads mapping (library information) or longer reads.
2019-06-27 17:25:19,502 - INFO: Writing PATH1 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.1.path_sequence.fasta
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2019-06-27 17:25:22,103 - INFO: Writing PATH379 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.379.path_sequence.fasta
2019-06-27 17:25:22,110 - INFO: Writing PATH380 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.380.path_sequence.fasta
2019-06-27 17:25:22,116 - INFO: Writing PATH381 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.381.path_sequence.fasta
2019-06-27 17:25:22,123 - INFO: Writing PATH382 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.382.path_sequence.fasta
2019-06-27 17:25:22,130 - INFO: Writing PATH383 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.383.path_sequence.fasta
2019-06-27 17:25:22,137 - INFO: Writing PATH384 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.384.path_sequence.fasta
2019-06-27 17:25:22,143 - INFO: Writing PATH385 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.385.path_sequence.fasta
2019-06-27 17:25:22,162 - INFO: Writing PATH386 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.386.path_sequence.fasta
2019-06-27 17:25:22,168 - INFO: Writing PATH387 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.387.path_sequence.fasta
2019-06-27 17:25:22,175 - INFO: Writing PATH388 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.388.path_sequence.fasta
2019-06-27 17:25:22,182 - INFO: Writing PATH389 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.389.path_sequence.fasta
2019-06-27 17:25:22,189 - INFO: Writing PATH390 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.390.path_sequence.fasta
2019-06-27 17:25:22,195 - INFO: Writing PATH391 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.391.path_sequence.fasta
2019-06-27 17:25:22,202 - INFO: Writing PATH392 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.392.path_sequence.fasta
2019-06-27 17:25:22,209 - INFO: Writing PATH393 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.393.path_sequence.fasta
2019-06-27 17:25:22,215 - INFO: Writing PATH394 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.394.path_sequence.fasta
2019-06-27 17:25:22,222 - INFO: Writing PATH395 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.395.path_sequence.fasta
2019-06-27 17:25:22,229 - INFO: Writing PATH396 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.396.path_sequence.fasta
2019-06-27 17:25:22,235 - INFO: Writing PATH397 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.397.path_sequence.fasta
2019-06-27 17:25:22,242 - INFO: Writing PATH398 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.398.path_sequence.fasta
2019-06-27 17:25:22,249 - INFO: Writing PATH399 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.399.path_sequence.fasta
2019-06-27 17:25:22,255 - INFO: Writing PATH400 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.400.path_sequence.fasta
2019-06-27 17:25:22,262 - INFO: Writing PATH401 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.401.path_sequence.fasta
2019-06-27 17:25:22,269 - INFO: Writing PATH402 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.402.path_sequence.fasta
2019-06-27 17:25:22,276 - INFO: Writing PATH403 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.403.path_sequence.fasta
2019-06-27 17:25:22,283 - INFO: Writing PATH404 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.404.path_sequence.fasta
2019-06-27 17:25:22,290 - INFO: Writing PATH405 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.405.path_sequence.fasta
2019-06-27 17:25:22,297 - INFO: Writing PATH406 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.406.path_sequence.fasta
2019-06-27 17:25:22,304 - INFO: Writing PATH407 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.407.path_sequence.fasta
2019-06-27 17:25:22,310 - INFO: Writing PATH408 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.408.path_sequence.fasta
2019-06-27 17:25:22,317 - INFO: Writing PATH409 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.409.path_sequence.fasta
2019-06-27 17:25:22,324 - INFO: Writing PATH410 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.410.path_sequence.fasta
2019-06-27 17:25:22,331 - INFO: Writing PATH411 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.411.path_sequence.fasta
2019-06-27 17:25:22,337 - INFO: Writing PATH412 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.412.path_sequence.fasta
2019-06-27 17:25:22,344 - INFO: Writing PATH413 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.413.path_sequence.fasta
2019-06-27 17:25:22,351 - INFO: Writing PATH414 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.414.path_sequence.fasta
2019-06-27 17:25:22,358 - INFO: Writing PATH415 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.415.path_sequence.fasta
2019-06-27 17:25:22,365 - INFO: Writing PATH416 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.416.path_sequence.fasta
2019-06-27 17:25:22,373 - INFO: Writing PATH417 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.417.path_sequence.fasta
2019-06-27 17:25:22,379 - INFO: Writing PATH418 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.418.path_sequence.fasta
2019-06-27 17:25:22,386 - INFO: Writing PATH419 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.419.path_sequence.fasta
2019-06-27 17:25:22,393 - INFO: Writing PATH420 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.420.path_sequence.fasta
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2019-06-27 17:25:22,660 - INFO: Writing PATH459 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.459.path_sequence.fasta
2019-06-27 17:25:22,666 - INFO: Writing PATH460 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.460.path_sequence.fasta
2019-06-27 17:25:22,673 - INFO: Writing PATH461 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.461.path_sequence.fasta
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2019-06-27 17:25:22,727 - INFO: Writing PATH469 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.469.path_sequence.fasta
2019-06-27 17:25:22,733 - INFO: Writing PATH470 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.470.path_sequence.fasta
2019-06-27 17:25:22,740 - INFO: Writing PATH471 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.471.path_sequence.fasta
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2019-06-27 17:25:22,753 - INFO: Writing PATH473 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.473.path_sequence.fasta
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2019-06-27 17:25:22,780 - INFO: Writing PATH477 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.477.path_sequence.fasta
2019-06-27 17:25:22,787 - INFO: Writing PATH478 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.478.path_sequence.fasta
2019-06-27 17:25:22,794 - INFO: Writing PATH479 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.479.path_sequence.fasta
2019-06-27 17:25:22,800 - INFO: Writing PATH480 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.480.path_sequence.fasta
2019-06-27 17:25:22,807 - INFO: Writing PATH481 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.481.path_sequence.fasta
2019-06-27 17:25:22,814 - INFO: Writing PATH482 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.482.path_sequence.fasta
2019-06-27 17:25:22,821 - INFO: Writing PATH483 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.483.path_sequence.fasta
2019-06-27 17:25:22,828 - INFO: Writing PATH484 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.484.path_sequence.fasta
2019-06-27 17:25:22,835 - INFO: Writing PATH485 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.485.path_sequence.fasta
2019-06-27 17:25:22,842 - INFO: Writing PATH486 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.486.path_sequence.fasta
2019-06-27 17:25:22,849 - INFO: Writing PATH487 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.487.path_sequence.fasta
2019-06-27 17:25:22,856 - INFO: Writing PATH488 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.488.path_sequence.fasta
2019-06-27 17:25:22,863 - INFO: Writing PATH489 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.489.path_sequence.fasta
2019-06-27 17:25:22,870 - INFO: Writing PATH490 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.490.path_sequence.fasta
2019-06-27 17:25:22,877 - INFO: Writing PATH491 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.491.path_sequence.fasta
2019-06-27 17:25:22,884 - INFO: Writing PATH492 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.492.path_sequence.fasta
2019-06-27 17:25:22,891 - INFO: Writing PATH493 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.493.path_sequence.fasta
2019-06-27 17:25:22,898 - INFO: Writing PATH494 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.494.path_sequence.fasta
2019-06-27 17:25:22,905 - INFO: Writing PATH495 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.495.path_sequence.fasta
2019-06-27 17:25:22,911 - INFO: Writing PATH496 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.496.path_sequence.fasta
2019-06-27 17:25:22,918 - INFO: Writing PATH497 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.497.path_sequence.fasta
2019-06-27 17:25:22,925 - INFO: Writing PATH498 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.498.path_sequence.fasta
2019-06-27 17:25:22,932 - INFO: Writing PATH499 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.499.path_sequence.fasta
2019-06-27 17:25:22,939 - INFO: Writing PATH500 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.500.path_sequence.fasta
2019-06-27 17:25:22,946 - INFO: Writing PATH501 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.501.path_sequence.fasta
2019-06-27 17:25:22,953 - INFO: Writing PATH502 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.502.path_sequence.fasta
2019-06-27 17:25:22,959 - INFO: Writing PATH503 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.503.path_sequence.fasta
2019-06-27 17:25:22,966 - INFO: Writing PATH504 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.504.path_sequence.fasta
2019-06-27 17:25:22,973 - INFO: Writing PATH505 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.505.path_sequence.fasta
2019-06-27 17:25:22,979 - INFO: Writing PATH506 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.506.path_sequence.fasta
2019-06-27 17:25:22,986 - INFO: Writing PATH507 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.507.path_sequence.fasta
2019-06-27 17:25:22,992 - INFO: Writing PATH508 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.508.path_sequence.fasta
2019-06-27 17:25:22,999 - INFO: Writing PATH509 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.509.path_sequence.fasta
2019-06-27 17:25:23,006 - INFO: Writing PATH510 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.510.path_sequence.fasta
2019-06-27 17:25:23,013 - INFO: Writing PATH511 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.511.path_sequence.fasta
2019-06-27 17:25:23,019 - INFO: Writing PATH512 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.512.path_sequence.fasta
2019-06-27 17:25:23,020 - INFO: Writing GRAPH to plastome_output2/embplant_pt.K85.complete.graph1.selected_graph.gfa
2019-06-27 17:25:23,066 - INFO: Result status of embplant_pt: circular genome
2019-06-27 17:25:23,226 - INFO: Please visualize plastome_output2/filtered_K85.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg using Bandage to confirm the final result.
2019-06-27 17:25:23,227 - INFO: Writing output finished.
2019-06-27 17:25:23,229 - INFO: Extracting embplant_pt from the assemblies finished.
Total cost 2605.14 s
Thank you!
And the resulting assembly in Bandage was as follows:
The text was updated successfully, but these errors were encountered: