[2024-01-24 12:54:39,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference
[2024-01-24 12:54:40,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:40,991] [INFO] Task started: Prodigal
[2024-01-24 12:54:40,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ad93383-e2cf-47d8-bc90-2d70de8d1af8/GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/cds.fna -a GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:51,738] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:51,738] [INFO] Task started: HMMsearch
[2024-01-24 12:54:51,739] [INFO] Running command: hmmsearch --tblout GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference/reference_markers.hmm GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:52,018] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:52,022] [INFO] Found 6/6 markers.
[2024-01-24 12:54:52,056] [INFO] Query marker FASTA was written to GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:54:52,056] [INFO] Task started: Blastn
[2024-01-24 12:54:52,057] [INFO] Running command: blastn -query GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference/reference_markers.fasta -out GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:52,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:52,798] [INFO] Selected 23 target genomes.
[2024-01-24 12:54:52,799] [INFO] Target genome list was writen to GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:54:52,806] [INFO] Task started: fastANI
[2024-01-24 12:54:52,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad93383-e2cf-47d8-bc90-2d70de8d1af8/GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna.gz --refList GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:09,095] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:09,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:09,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:09,112] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:55:09,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:09,113] [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
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	100.0	1083	1089	95	conclusive
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	79.7565	437	1089	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.3807	139	1089	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.093	235	1089	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.6804	237	1089	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.6562	225	1089	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.6416	143	1089	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.6309	244	1089	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.5377	210	1089	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.4478	148	1089	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.4192	260	1089	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.4059	219	1089	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.2665	225	1089	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.2481	186	1089	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	77.2115	214	1089	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	77.1727	221	1089	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	77.1372	142	1089	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.0292	192	1089	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	77.0083	159	1089	95	below_threshold
Pseudorhodobacter aquimaris	strain=KCTC 23043	GCA_001202025.1	687412	687412	type	True	76.9834	107	1089	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.9318	201	1089	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	76.9262	121	1089	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.3418	92	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:09,115] [INFO] DFAST Taxonomy check result was written to GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:55:09,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:09,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:09,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference/checkm_data
[2024-01-24 12:55:09,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:09,155] [INFO] Task started: CheckM
[2024-01-24 12:55:09,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/checkm_input GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:55:44,432] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:44,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:44,456] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:44,456] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:44,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:55:44,457] [INFO] Task started: Blastn
[2024-01-24 12:55:44,457] [INFO] Running command: blastn -query GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg817b8f93-8bc8-4bcf-9f73-acc05595ef56/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:45,443] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:45,447] [INFO] Selected 21 target genomes.
[2024-01-24 12:55:45,447] [INFO] Target genome list was writen to GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:45,464] [INFO] Task started: fastANI
[2024-01-24 12:55:45,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad93383-e2cf-47d8-bc90-2d70de8d1af8/GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna.gz --refList GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:00,286] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:00,309] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:00,310] [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_900129685.1	s__Cognatishimia maritima	100.0	1082	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001458335.1	s__Cognatishimia activa	79.7483	438	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCF_017798205.1	s__Cognatishimia activa_A	78.7211	333	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215215.1	s__Cognatishimia sp013215215	78.3941	313	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	78.0214	234	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_900114635.1	s__Shimia aestuarii	77.9953	259	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496005.1	s__Epibacterium litoralis	77.8665	216	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	77.7985	305	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_017744095.1	s__Shimia sp017744095	77.7094	259	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	77.6864	236	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_900302455.1	s__Ruegeria_E mediterranea	77.5319	209	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCA_900143635.1	s__FREY01 sp900143635	77.529	226	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__FREY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102795.1	s__Epibacterium ulvae	77.4793	160	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900172225.1	s__Ruegeria_E litorea	77.4059	219	1089	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_001679925.1	s__Leisingera sp001679925	77.2473	224	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143615.1	s__Shimia sp900143615	77.2242	202	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014475.1	s__Shimia abyssi	77.1855	220	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.0721	187	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001507595.1	s__Ruegeria marisrubri	77.0292	192	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122245.1	s__Roseovarius sp003122245	76.4609	125	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440625.1	s__Albidovulum sp002440625	75.8277	59	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:00,311] [INFO] GTDB search result was written to GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:00,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:00,316] [INFO] DFAST_QC result json was written to GCF_900129685.1_IMG-taxon_2617270829_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:56:00,317] [INFO] DFAST_QC completed!
[2024-01-24 12:56:00,317] [INFO] Total running time: 0h1m21s