[2024-01-24 11:51:24,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference
[2024-01-24 11:51:26,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,172] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg7db57730-773e-402d-ada0-ce5ab0e02de6/GCF_018263925.1_ASM1826392v1_genomic.fna.gz | prodigal -d GCF_018263925.1_ASM1826392v1_genomic.fna/cds.fna -a GCF_018263925.1_ASM1826392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:41,113] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:41,114] [INFO] Task started: HMMsearch
[2024-01-24 11:51:41,114] [INFO] Running command: hmmsearch --tblout GCF_018263925.1_ASM1826392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference/reference_markers.hmm GCF_018263925.1_ASM1826392v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:41,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:41,415] [INFO] Found 6/6 markers.
[2024-01-24 11:51:41,466] [INFO] Query marker FASTA was written to GCF_018263925.1_ASM1826392v1_genomic.fna/markers.fasta
[2024-01-24 11:51:41,466] [INFO] Task started: Blastn
[2024-01-24 11:51:41,466] [INFO] Running command: blastn -query GCF_018263925.1_ASM1826392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference/reference_markers.fasta -out GCF_018263925.1_ASM1826392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:42,283] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:42,286] [INFO] Selected 25 target genomes.
[2024-01-24 11:51:42,287] [INFO] Target genome list was writen to GCF_018263925.1_ASM1826392v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:42,296] [INFO] Task started: fastANI
[2024-01-24 11:51:42,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg7db57730-773e-402d-ada0-ce5ab0e02de6/GCF_018263925.1_ASM1826392v1_genomic.fna.gz --refList GCF_018263925.1_ASM1826392v1_genomic.fna/target_genomes.txt --output GCF_018263925.1_ASM1826392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:01,279] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:01,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:01,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:01,296] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:01,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:01,297] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Kistimonas asteriae	strain=KMD 001	GCA_018263925.1	517724	517724	type	True	100.0	1646	1649	95	conclusive
Sansalvadorimonas verongulae	strain=RKSG058	GCA_009711465.1	2172824	2172824	type	True	77.5755	121	1649	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.4209	105	1649	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	77.3833	87	1649	95	below_threshold
Parendozoicomonas haliclonae		GCA_900174585.1	1960125	1960125	type	True	77.3527	154	1649	95	below_threshold
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	77.2514	107	1649	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	77.2372	105	1649	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_001411965.1	47879	47879	type	True	76.8251	56	1649	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	76.7655	115	1649	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.5783	71	1649	95	below_threshold
Aestuariirhabdus litorea	strain=GTF13	GCA_003864255.1	2528527	2528527	type	True	76.5706	84	1649	95	below_threshold
Pseudomonas mediterranea	strain=DSM 16733	GCA_900106005.1	183795	183795	type	True	76.5626	63	1649	95	below_threshold
Pseudomonas fluvialis	strain=ASS-1	GCA_002234375.1	1793966	1793966	suspected-type	True	76.562	70	1649	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.5273	68	1649	95	below_threshold
Pseudomonas mediterranea	strain=CFBP 5447	GCA_000774145.1	183795	183795	type	True	76.5261	61	1649	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	76.4797	57	1649	95	below_threshold
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	76.4671	72	1649	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	76.465	64	1649	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.4306	76	1649	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	76.3055	70	1649	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	76.3001	65	1649	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	76.055	58	1649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:01,298] [INFO] DFAST Taxonomy check result was written to GCF_018263925.1_ASM1826392v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:01,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:01,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:01,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference/checkm_data
[2024-01-24 11:52:01,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:01,355] [INFO] Task started: CheckM
[2024-01-24 11:52:01,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018263925.1_ASM1826392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018263925.1_ASM1826392v1_genomic.fna/checkm_input GCF_018263925.1_ASM1826392v1_genomic.fna/checkm_result
[2024-01-24 11:52:50,238] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:50,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:50,262] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:50,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:50,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018263925.1_ASM1826392v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:50,263] [INFO] Task started: Blastn
[2024-01-24 11:52:50,264] [INFO] Running command: blastn -query GCF_018263925.1_ASM1826392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e93625-72a1-48f2-a286-5235d7c5f1cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_018263925.1_ASM1826392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:51,625] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:51,628] [INFO] Selected 21 target genomes.
[2024-01-24 11:52:51,629] [INFO] Target genome list was writen to GCF_018263925.1_ASM1826392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:51,655] [INFO] Task started: fastANI
[2024-01-24 11:52:51,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg7db57730-773e-402d-ada0-ce5ab0e02de6/GCF_018263925.1_ASM1826392v1_genomic.fna.gz --refList GCF_018263925.1_ASM1826392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018263925.1_ASM1826392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:09,233] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:09,262] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:09,262] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_018263925.1	s__Kistimonas asteriae	100.0	1646	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002084115.1	s__Kistimonas sp002084115	88.6717	740	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647025.1	s__Endozoicomonas atrinae	77.4096	108	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562015.1	s__Endozoicomonas arenosclerae	77.3629	85	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900174585.1	s__Parendozoicomonas haliclonae	77.332	151	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Parendozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583435.1	s__Endozoicomonas montiporae	77.2122	106	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
GCF_009653635.1	s__Endozoicomonas sp009653635	77.0126	89	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269905.1	s__Pseudomonas_E corrugata	76.9523	59	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.47	0.98	0.95	7	-
GCA_017744115.1	s__Endozoicomonas sp017744115	76.7815	120	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCF_002864045.1	s__Endozoicomonas acroporae	76.7409	113	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	-
GCF_003864255.1	s__Aestuariirhabdus litorea	76.5755	84	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Aestuariirhabdaceae;g__Aestuariirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007828215.1	s__Pseudomonas_E sp007828215	76.5206	53	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	99.65	0.96	0.95	6	-
GCF_000364845.1	s__Marinobacter_A nanhaiticus	76.4797	57	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.4547	75	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_000418555.1	s__Pseudomonas_E sp000418555	76.4028	74	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013386585.1	s__Pseudomonas_E sp013386585	76.3959	65	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009861525.1	s__Pseudomonas_E sp009861525	76.3256	63	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111835.1	s__Pseudomonas_F otitidis	76.1585	73	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	76.0703	74	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080045.1	s__Pseudomonas_E sp002080045	76.0698	50	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:09,264] [INFO] GTDB search result was written to GCF_018263925.1_ASM1826392v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:09,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:09,271] [INFO] DFAST_QC result json was written to GCF_018263925.1_ASM1826392v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:09,271] [INFO] DFAST_QC completed!
[2024-01-24 11:53:09,271] [INFO] Total running time: 0h1m44s