[2024-01-24 12:06:10,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference
[2024-01-24 12:06:13,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,065] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg18733bde-d881-4ffa-8314-2281a01bd852/GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/cds.fna -a GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,758] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,758] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,758] [INFO] Running command: hmmsearch --tblout GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference/reference_markers.hmm GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,100] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,102] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,141] [INFO] Query marker FASTA was written to GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 12:06:28,141] [INFO] Task started: Blastn
[2024-01-24 12:06:28,141] [INFO] Running command: blastn -query GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference/reference_markers.fasta -out GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:28,969] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:28,972] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:28,972] [INFO] Target genome list was writen to GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 12:06:28,977] [INFO] Task started: fastANI
[2024-01-24 12:06:28,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg18733bde-d881-4ffa-8314-2281a01bd852/GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna.gz --refList GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:42,212] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:42,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:42,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:42,226] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:42,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:42,227] [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
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	100.0	1427	1429	95	conclusive
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	82.3522	777	1429	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	82.3435	785	1429	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.2359	623	1429	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	79.019	588	1429	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.4746	417	1429	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	78.3878	378	1429	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	78.2047	338	1429	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.2009	365	1429	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	78.1525	500	1429	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4945	357	1429	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.4724	293	1429	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.6691	205	1429	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.4983	213	1429	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.252	171	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:42,228] [INFO] DFAST Taxonomy check result was written to GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 12:06:42,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:42,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:42,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference/checkm_data
[2024-01-24 12:06:42,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:42,280] [INFO] Task started: CheckM
[2024-01-24 12:06:42,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/checkm_input GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 12:07:29,073] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:29,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:29,097] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:29,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:29,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 12:07:29,098] [INFO] Task started: Blastn
[2024-01-24 12:07:29,099] [INFO] Running command: blastn -query GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg44a6349c-8159-4f51-a18c-7d8d6ac153e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:30,232] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:30,238] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:30,238] [INFO] Target genome list was writen to GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:30,250] [INFO] Task started: fastANI
[2024-01-24 12:07:30,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg18733bde-d881-4ffa-8314-2281a01bd852/GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna.gz --refList GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:42,707] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:42,732] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:42,732] [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_001458255.1	s__Thalassobius autumnalis	100.0	1427	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCF_001458435.1	s__Thalassobius mediterraneus	82.3321	779	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857745.1	s__Thalassobius mangrovi	79.2135	626	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	79.0112	589	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	78.8807	413	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_900182725.1	s__Thalassobius litoralis	78.613	433	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	78.4826	415	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	78.3863	377	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	78.326	448	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017792425.1	s__Thalassobius sp017792425	78.2683	437	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	78.1977	366	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458355.1	s__Thalassobius gelatinovorus	78.1944	492	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCF_001507595.1	s__Ruegeria marisrubri	78.0006	366	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872815.1	s__Shimia sp014872815	77.9399	346	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	97.10	97.10	0.91	0.91	2	-
GCF_017744095.1	s__Shimia sp017744095	77.8982	361	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	77.8493	350	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:42,734] [INFO] GTDB search result was written to GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:42,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:42,738] [INFO] DFAST_QC result json was written to GCF_001458255.1_Tmediterraneus_CECT5118_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 12:07:42,738] [INFO] DFAST_QC completed!
[2024-01-24 12:07:42,738] [INFO] Total running time: 0h1m32s