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Strange output - is it normal? #38

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Gian77 opened this issue Jan 26, 2023 · 2 comments
Closed

Strange output - is it normal? #38

Gian77 opened this issue Jan 26, 2023 · 2 comments
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@oschwengers
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help wanted Extra attention is needed

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@Gian77
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Gian77 commented Jan 26, 2023

Hello,

First of all, thanks for this tool, I think it is really important to identify plasmid-related contigs. I am running platon on a series of genome contigs files. The tool is able find several contigs, in different genomes, that are plasmid-borne.

However, in some of the genomes I have this results below, and I am not sure if it is normal or not? I wish there was something prompted like, for example >>> ANALYSIS COMPLETED SUCCESSFULLY >>> or similar sentence, to understand if the tool run correctly or not.

And example of what I mean is this output:

(platon) [gian@dev-amd20 code]$ platon /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/assembly.fasta --threads 40 --verbose --db /mnt/research/ShadeLab/gian/databases/platon_db/db/ --output /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/
Platon v1.6
Options and arguments:
   input: /mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/contigs_hq_fixstart.fasta
   db: /mnt/ufs18/rs-033/ShadeLab/gian/databases/platon_db/db
   output: /mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2
   prefix: assembly
   mode: accuracy
   characterize: False
   tmp path: /tmp/tmpz4iqsjqa
   # threads: 40
parse draft genome...
   exclude contig 'NODE_1_length_2147114_cov_45.153046', too long (2147114)
   exclude contig 'NODE_20_length_823_cov_292.701149', too short (823)
   exclude contig 'NODE_21_length_695_cov_331.225352', too short (695)
   exclude contig 'NODE_23_length_574_cov_71.671141', too short (574)
   exclude contig 'NODE_24_length_548_cov_296.399050', too short (548)
   exclude contig 'NODE_25_length_527_cov_299.475000', too short (527)
   exclude contig 'NODE_26_length_518_cov_40.744246', too short (518)
   exclude contig 'NODE_2_length_513869_cov_43.096975', too long (513869)
   parsed 22 raw contigs
   excluded 8 contigs by size filter
   analyze 14 contigs
predict ORFs...
   found 1909 ORFs
search marker protein sequences (MPS)...
   found 1730 MPS
compute replicon distribution scores (RDS)...
apply RDS sensitivity threshold (SNT=-7.9) filter...
   excluded 9 contigs by SNT filter
characterize contigs...
ID	Length	Coverage	# ORFs	RDS	Circular	Inc Type(s)	# Replication	# Mobilization	# OriT	# Conjugation	# AMRs	# rRNAs	# Plasmid Hits

and if I look in the output directory I have:

(platon) [gian@dev-amd20 code]$ ll /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/
total 4.7M
-rw-r----- 1 gian ShadeLab 4.6M Jan 25 21:00 assembly.chromosome.fasta
-rw-r----- 1 gian ShadeLab    2 Jan 25 21:00 assembly.json
-rw-r----- 1 gian ShadeLab  11K Jan 25 21:00 assembly.log
-rw-r----- 1 gian ShadeLab    0 Jan 25 21:00 assembly.plasmid.fasta
-rw-r----- 1 gian ShadeLab  131 Jan 25 21:00 assembly.tsv

and

(platon) [gian@dev-amd20 code]$ cat /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/assembly.log 
2023-01-25 21:00:02,269 - INFO - MAIN - version 1.6
2023-01-25 21:00:02,270 - INFO - MAIN - command line: /mnt/home/gian/anaconda2/envs/platon/bin/platon /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/assembly.fasta --threads 40 --verbose --db /mnt/research/ShadeLab/gian/databases/platon_db/db/ --output /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/
2023-01-25 21:00:02,270 - INFO - CONFIG - threads=40
2023-01-25 21:00:02,270 - INFO - CONFIG - verbose=True
2023-01-25 21:00:02,270 - DEBUG - CONFIG - test parameter db: db_tmp=/mnt/research/ShadeLab/gian/databases/platon_db/db/
2023-01-25 21:00:02,271 - INFO - CONFIG - database detected: type=parameter, path=/mnt/ufs18/rs-033/ShadeLab/gian/databases/platon_db/db
2023-01-25 21:00:02,271 - INFO - CONFIG - genome-path=/mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/contigs_hq_fixstart.fasta
2023-01-25 21:00:02,272 - INFO - CONFIG - tmp-path=/tmp/tmpz4iqsjqa
2023-01-25 21:00:02,272 - INFO - CONFIG - output-path=/mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2
2023-01-25 21:00:02,272 - INFO - CONFIG - mode=accuracy
2023-01-25 21:00:02,272 - INFO - CONFIG - characterize=False
2023-01-25 21:00:02,289 - INFO - UTILS - dependency check: tool=prodigal, version=v2.6.3
2023-01-25 21:00:02,295 - INFO - UTILS - dependency check: tool=diamond, version=v2.0.15
2023-01-25 21:00:02,355 - INFO - UTILS - dependency check: tool=blastn, version=v2.12.0
2023-01-25 21:00:02,359 - INFO - UTILS - dependency check: tool=hmmsearch, version=v3.3.2
2023-01-25 21:00:02,363 - INFO - UTILS - dependency check: tool=nucmer, version=v4.0.0
2023-01-25 21:00:02,368 - INFO - UTILS - dependency check: tool=cmscan, version=v1.1.4
2023-01-25 21:00:02,405 - INFO - MAIN - exclude contig: too long: id=NODE_1_length_2147114_cov_45.153046, length=2147114
2023-01-25 21:00:02,406 - INFO - MAIN - exclude contig: too short: id=NODE_20_length_823_cov_292.701149, length=823
2023-01-25 21:00:02,407 - INFO - MAIN - exclude contig: too short: id=NODE_21_length_695_cov_331.225352, length=695
2023-01-25 21:00:02,407 - INFO - MAIN - exclude contig: too short: id=NODE_23_length_574_cov_71.671141, length=574
2023-01-25 21:00:02,407 - INFO - MAIN - exclude contig: too short: id=NODE_24_length_548_cov_296.399050, length=548
2023-01-25 21:00:02,407 - INFO - MAIN - exclude contig: too short: id=NODE_25_length_527_cov_299.475000, length=527
2023-01-25 21:00:02,408 - INFO - MAIN - exclude contig: too short: id=NODE_26_length_518_cov_40.744246, length=518
2023-01-25 21:00:02,413 - INFO - MAIN - exclude contig: too long: id=NODE_2_length_513869_cov_43.096975, length=513869
2023-01-25 21:00:02,429 - INFO - MAIN - length contig filter: # input=22, # discarded=8, # remaining=14
2023-01-25 21:00:10,088 - INFO - MAIN - ORF detection: # ORFs=1909
2023-01-25 21:00:10,088 - INFO - MAIN - ORF contig filter disabled! # passed contigs=14
2023-01-25 21:00:19,642 - INFO - MAIN - MPS detection: # MPS=1730
2023-01-25 21:00:25,249 - INFO - MAIN - contig RDS: contig=NODE_10_length_166327_cov_45.482142, RDS=-23.173201, score-sum=-3499.153336, #ORFs=151
2023-01-25 21:00:25,256 - INFO - MAIN - contig RDS: contig=NODE_11_length_115072_cov_45.243195, RDS=-15.155100, score-sum=-1636.750778, #ORFs=108
2023-01-25 21:00:25,257 - INFO - MAIN - contig RDS: contig=NODE_12_length_66594_cov_47.770924, RDS=-3.705217, score-sum=-207.492140, #ORFs=56
2023-01-25 21:00:25,258 - INFO - MAIN - contig RDS: contig=NODE_13_length_60171_cov_42.250333, RDS=-40.436105, score-sum=-2223.985785, #ORFs=55
2023-01-25 21:00:25,259 - INFO - MAIN - contig RDS: contig=NODE_14_length_40297_cov_44.013343, RDS=0.590191, score-sum=17.705734, #ORFs=30
2023-01-25 21:00:25,260 - INFO - MAIN - contig RDS: contig=NODE_15_length_31833_cov_44.891125, RDS=-116.252568, score-sum=-3255.071897, #ORFs=28
2023-01-25 21:00:25,260 - INFO - MAIN - contig RDS: contig=NODE_18_length_1134_cov_125.804369, RDS=0.000000, score-sum=0.000000, #ORFs=0
2023-01-25 21:00:25,260 - INFO - MAIN - contig RDS: contig=NODE_19_length_1061_cov_304.962527, RDS=0.000000, score-sum=0.000000, #ORFs=0
2023-01-25 21:00:25,263 - INFO - MAIN - contig RDS: contig=NODE_3_length_435256_cov_45.365944, RDS=-18.422025, score-sum=-7147.745700, #ORFs=388
2023-01-25 21:00:25,266 - INFO - MAIN - contig RDS: contig=NODE_4_length_347418_cov_46.100826, RDS=-17.713544, score-sum=-5367.203949, #ORFs=303
2023-01-25 21:00:25,267 - INFO - MAIN - contig RDS: contig=NODE_6_length_258053_cov_46.234761, RDS=-15.931166, score-sum=-3377.407243, #ORFs=212
2023-01-25 21:00:25,269 - INFO - MAIN - contig RDS: contig=NODE_7_length_218603_cov_46.117441, RDS=-15.435090, score-sum=-3009.842526, #ORFs=195
2023-01-25 21:00:25,270 - INFO - MAIN - contig RDS: contig=NODE_8_length_203124_cov_45.556353, RDS=0.369013, score-sum=63.470272, #ORFs=172
2023-01-25 21:00:25,272 - INFO - MAIN - contig RDS: contig=NODE_9_length_201256_cov_45.789384, RDS=-84.505940, score-sum=-17830.753259, #ORFs=211
2023-01-25 21:00:25,273 - INFO - MAIN - RDS SNT filter: # discarded contigs=9, # remaining contigs=5
2023-01-25 21:00:25,315 - DEBUG - functions - circularity: contig=NODE_12_length_66594_cov_47.770924, len=66594, seq-a-len=33297, seq-b-len=33297
2023-01-25 21:00:25,326 - DEBUG - functions - circularity: contig=NODE_14_length_40297_cov_44.013343, len=40297, seq-a-len=20148, seq-b-len=20149
2023-01-25 21:00:25,326 - DEBUG - functions - circularity: contig=NODE_18_length_1134_cov_125.804369, len=1134, seq-a-len=567, seq-b-len=567
2023-01-25 21:00:25,334 - DEBUG - functions - circularity: contig=NODE_19_length_1061_cov_304.962527, len=1061, seq-a-len=530, seq-b-len=531
2023-01-25 21:00:25,339 - DEBUG - functions - circularity: contig=NODE_8_length_203124_cov_45.556353, len=203124, seq-a-len=101562, seq-b-len=101562
2023-01-25 21:00:25,343 - INFO - functions - circularity: contig=NODE_12_length_66594_cov_47.770924, is-circ=False
2023-01-25 21:00:25,344 - INFO - functions - circularity: contig=NODE_18_length_1134_cov_125.804369, is-circ=False
2023-01-25 21:00:25,346 - INFO - functions - circularity: contig=NODE_14_length_40297_cov_44.013343, is-circ=False
2023-01-25 21:00:25,348 - INFO - functions - circularity: contig=NODE_19_length_1061_cov_304.962527, is-circ=False
2023-01-25 21:00:25,379 - INFO - functions - circularity: contig=NODE_8_length_203124_cov_45.556353, is-circ=False
2023-01-25 21:00:25,466 - INFO - functions - oriT: contig=NODE_12_length_66594_cov_47.770924, # oriT=0
2023-01-25 21:00:25,486 - INFO - functions - oriT: contig=NODE_18_length_1134_cov_125.804369, # oriT=0
2023-01-25 21:00:25,487 - INFO - functions - oriT: contig=NODE_19_length_1061_cov_304.962527, # oriT=0
2023-01-25 21:00:25,491 - INFO - functions - oriT: contig=NODE_14_length_40297_cov_44.013343, # oriT=0
2023-01-25 21:00:25,513 - INFO - functions - oriT: contig=NODE_8_length_203124_cov_45.556353, # oriT=0
2023-01-25 21:00:25,572 - INFO - functions - inc-type: contig=NODE_19_length_1061_cov_304.962527, # inc-types=0
2023-01-25 21:00:25,578 - INFO - functions - inc-type: contig=NODE_14_length_40297_cov_44.013343, # inc-types=0
2023-01-25 21:00:25,579 - INFO - functions - inc-type: contig=NODE_8_length_203124_cov_45.556353, # inc-types=0
2023-01-25 21:00:25,591 - INFO - functions - inc-type: contig=NODE_18_length_1134_cov_125.804369, # inc-types=0
2023-01-25 21:00:25,591 - INFO - functions - inc-type: contig=NODE_12_length_66594_cov_47.770924, # inc-types=0
2023-01-25 21:00:25,763 - INFO - functions - rRNAs: contig=NODE_14_length_40297_cov_44.013343, # rRNAs=0
2023-01-25 21:00:25,770 - INFO - functions - ref plasmids: contig=NODE_12_length_66594_cov_47.770924, # ref plasmids=0
2023-01-25 21:00:25,770 - INFO - functions - ref plasmids: contig=NODE_8_length_203124_cov_45.556353, # ref plasmids=0
2023-01-25 21:00:25,850 - INFO - functions - ref plasmids: contig=NODE_14_length_40297_cov_44.013343, # ref plasmids=0
2023-01-25 21:00:26,072 - INFO - functions - rRNAs: hit! contig=NODE_18_length_1134_cov_125.804369, type=LSU_rRNA_bacteria, start=661, end=1134, strand=+
2023-01-25 21:00:26,072 - INFO - functions - rRNAs: hit! contig=NODE_18_length_1134_cov_125.804369, type=SSU_rRNA_bacteria, start=1, end=82, strand=+
2023-01-25 21:00:26,074 - INFO - functions - rRNAs: contig=NODE_18_length_1134_cov_125.804369, # rRNAs=2
2023-01-25 21:00:26,163 - INFO - functions - rRNAs: contig=NODE_12_length_66594_cov_47.770924, # rRNAs=0
2023-01-25 21:00:26,868 - INFO - functions - ref plasmids: hit! contig=NODE_19_length_1061_cov_304.962527, id=NZ_AP023206.1, c-start=6, c-end=1054, coverage=0.988690, identity=0.968541
2023-01-25 21:00:26,868 - INFO - functions - ref plasmids: contig=NODE_19_length_1061_cov_304.962527, # ref plasmids=1
2023-01-25 21:00:26,883 - INFO - functions - ref plasmids: contig=NODE_18_length_1134_cov_125.804369, # ref plasmids=0
2023-01-25 21:00:27,438 - INFO - functions - AMRs: hit! contig=NODE_8_length_203124_cov_45.556353, type=RND_permease_1-NCBI, start=10910, end=14014, strand=+
2023-01-25 21:00:27,438 - INFO - functions - AMRs: contig=NODE_8_length_203124_cov_45.556353, # AMRs=1
2023-01-25 21:00:28,073 - INFO - functions - rRNAs: hit! contig=NODE_19_length_1061_cov_304.962527, type=LSU_rRNA_bacteria, start=1, end=1035, strand=+
2023-01-25 21:00:28,076 - INFO - functions - rRNAs: contig=NODE_19_length_1061_cov_304.962527, # rRNAs=1
2023-01-25 21:00:28,476 - INFO - functions - rRNAs: contig=NODE_8_length_203124_cov_45.556353, # rRNAs=0
2023-01-25 21:00:29,547 - DEBUG - MAIN - removed tmp dir: /tmp/tmpz4iqsjqa
2023-01-25 21:00:29,548 - DEBUG - MAIN - output: tsv=/mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/assembly.tsv
2023-01-25 21:00:29,550 - DEBUG - MAIN - output: json=/mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/assembly.json
2023-01-25 21:00:29,552 - DEBUG - MAIN - output: chromosomes=/mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/assembly.chromosome.fasta
2023-01-25 21:00:29,562 - DEBUG - MAIN - output: plasmids=/mnt/ufs18/home-150/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/assembly.plasmid.fasta

and the ,tsv file is empty

(platon) [gian@dev-amd20 code]$ cat /mnt/home/gian/project_82_genomes/data/PvP012-Illumina_Pantoea_agglomerans_52616.3.395054.CTCATTGC-CTCATTGC_results/platon2/assembly.tsv 
ID	Length	Coverage	# ORFs	RDS	Circular	Inc Type(s)	# Replication	# Mobilization	# OriT	# Conjugation	# AMRs	# rRNAs	# Plasmid Hits

Thanks much!
Gian
@Gian77 Gian77 added the bug Something isn't working label Jan 26, 2023
@oschwengers oschwengers self-assigned this Jan 26, 2023
@oschwengers oschwengers added help wanted Extra attention is needed and removed bug Something isn't working labels Jan 26, 2023
@oschwengers
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Hi @Gian77, thanks for reaching out and asking.
Actually, Platon's behavior in this situation is correct and expected, however I totally agree that indeed it might leave users a little puzzled who might expect a different behavior.

Platon was designed to separate plasmid-born from chromosome-borne contigs in a fully-automated manner. Therefore, it creates both files assembly.chromosome.fasta and assembly.plasmid.fasta even thought all contigs are classified as chromosome-born and thus are written to the chromosome file. In your use case, Platon simply cannot find any plasmid-related contigs and thus classifies all contigs as chromosome-born. In this regard, it's the expected behavior as it separated all contigs and provides information on all plasmid-borne contigs (in this case, there are none).

I agree that the command line output might be confusing. I'll add a short message at the end explicitly stating that there were no plasmid-borne contigs detected.

Best regards!

@oschwengers oschwengers pinned this issue Jan 26, 2023
@Gian77
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Gian77 commented Jan 26, 2023

Hello @oschwengers,

Awesome, thanks a lot!

Gian

oschwengers added a commit that referenced this issue Jan 27, 2023
@oschwengers
print msg if no plasmid contigs were found #38
b896811
Taerim02 pushed a commit to Taerim02/platon that referenced this issue Feb 7, 2024
@oschwengers
print msg if no plasmid contigs were found oschwengers#38
46c0300
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