[2024-01-24 12:30:18,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference
[2024-01-24 12:30:20,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,238] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,238] [INFO] Running command: gunzip -c /var/lib/cwl/stge25da2cb-415a-4956-b75c-df08b81ce749/GCF_014651375.1_ASM1465137v1_genomic.fna.gz | prodigal -d GCF_014651375.1_ASM1465137v1_genomic.fna/cds.fna -a GCF_014651375.1_ASM1465137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:37,120] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:37,121] [INFO] Task started: HMMsearch
[2024-01-24 12:30:37,121] [INFO] Running command: hmmsearch --tblout GCF_014651375.1_ASM1465137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference/reference_markers.hmm GCF_014651375.1_ASM1465137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:37,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:37,424] [INFO] Found 6/6 markers.
[2024-01-24 12:30:37,469] [INFO] Query marker FASTA was written to GCF_014651375.1_ASM1465137v1_genomic.fna/markers.fasta
[2024-01-24 12:30:37,469] [INFO] Task started: Blastn
[2024-01-24 12:30:37,470] [INFO] Running command: blastn -query GCF_014651375.1_ASM1465137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference/reference_markers.fasta -out GCF_014651375.1_ASM1465137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:38,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:38,306] [INFO] Selected 25 target genomes.
[2024-01-24 12:30:38,306] [INFO] Target genome list was writen to GCF_014651375.1_ASM1465137v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:38,316] [INFO] Task started: fastANI
[2024-01-24 12:30:38,317] [INFO] Running command: fastANI --query /var/lib/cwl/stge25da2cb-415a-4956-b75c-df08b81ce749/GCF_014651375.1_ASM1465137v1_genomic.fna.gz --refList GCF_014651375.1_ASM1465137v1_genomic.fna/target_genomes.txt --output GCF_014651375.1_ASM1465137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:56,107] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:56,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:56,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:56,131] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:56,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:56,132] [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
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	100.0	1569	1571	95	conclusive
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.7353	334	1571	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.6726	281	1571	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.6421	346	1571	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.5503	350	1571	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.5477	256	1571	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.5434	259	1571	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.5114	259	1571	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.4766	318	1571	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.4563	312	1571	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.4019	183	1571	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.345	233	1571	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	77.2867	247	1571	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	77.2483	257	1571	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.2432	290	1571	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.2318	196	1571	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.1787	289	1571	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.1558	289	1571	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	77.0518	184	1571	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.9863	245	1571	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.9139	245	1571	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.7279	195	1571	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.7279	195	1571	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	76.7091	155	1571	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	76.6775	156	1571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:56,134] [INFO] DFAST Taxonomy check result was written to GCF_014651375.1_ASM1465137v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:56,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:56,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:56,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference/checkm_data
[2024-01-24 12:30:56,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:56,181] [INFO] Task started: CheckM
[2024-01-24 12:30:56,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651375.1_ASM1465137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651375.1_ASM1465137v1_genomic.fna/checkm_input GCF_014651375.1_ASM1465137v1_genomic.fna/checkm_result
[2024-01-24 12:31:52,420] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:52,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:52,445] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:52,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:52,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651375.1_ASM1465137v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:52,447] [INFO] Task started: Blastn
[2024-01-24 12:31:52,447] [INFO] Running command: blastn -query GCF_014651375.1_ASM1465137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8685f85-dae5-4148-8d48-967f4f2ba46b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651375.1_ASM1465137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:53,808] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:53,813] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:53,813] [INFO] Target genome list was writen to GCF_014651375.1_ASM1465137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:53,835] [INFO] Task started: fastANI
[2024-01-24 12:31:53,835] [INFO] Running command: fastANI --query /var/lib/cwl/stge25da2cb-415a-4956-b75c-df08b81ce749/GCF_014651375.1_ASM1465137v1_genomic.fna.gz --refList GCF_014651375.1_ASM1465137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651375.1_ASM1465137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:07,103] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:07,123] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:07,124] [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_014651375.1	s__Tateyamaria omphalii	100.0	1569	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000814025.1	s__Tateyamaria sp000814025	81.5423	859	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	81.3819	869	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	81.3407	879	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143535.1	s__Tateyamaria sp900143535	78.1403	488	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.4997	260	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004803475.1	s__Aliishimia ponticola	77.4735	320	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743995.1	s__Ruegeria sp017743995	77.4615	273	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	77.4155	265	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_900182615.1	s__Ruegeria faecimaris	77.3353	225	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.246	195	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	77.1483	172	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002405.1	s__Sulfitobacter sp013002405	77.1291	239	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	77.1049	275	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	77.0421	167	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.8477	189	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:07,125] [INFO] GTDB search result was written to GCF_014651375.1_ASM1465137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:07,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:07,132] [INFO] DFAST_QC result json was written to GCF_014651375.1_ASM1465137v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:07,132] [INFO] DFAST_QC completed!
[2024-01-24 12:32:07,132] [INFO] Total running time: 0h1m48s