[2024-01-24 14:11:46,562] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference
[2024-01-24 14:11:47,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,779] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,779] [INFO] Running command: gunzip -c /var/lib/cwl/stgf22ee9b1-7c3e-4de8-b196-daeca0135350/GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/cds.fna -a GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:01,339] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:01,340] [INFO] Task started: HMMsearch
[2024-01-24 14:12:01,340] [INFO] Running command: hmmsearch --tblout GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference/reference_markers.hmm GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:01,616] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:01,617] [INFO] Found 6/6 markers.
[2024-01-24 14:12:01,661] [INFO] Query marker FASTA was written to GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:01,662] [INFO] Task started: Blastn
[2024-01-24 14:12:01,662] [INFO] Running command: blastn -query GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference/reference_markers.fasta -out GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:02,456] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:02,461] [INFO] Selected 21 target genomes.
[2024-01-24 14:12:02,462] [INFO] Target genome list was writen to GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:02,479] [INFO] Task started: fastANI
[2024-01-24 14:12:02,479] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22ee9b1-7c3e-4de8-b196-daeca0135350/GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna.gz --refList GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:18,408] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:18,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:18,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:18,427] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:18,428] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:18,428] [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
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	100.0	1319	1325	95	conclusive
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	79.3164	548	1325	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	78.2509	376	1325	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.868	281	1325	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	77.8113	308	1325	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	77.6127	223	1325	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.5744	260	1325	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.5288	261	1325	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	77.4493	190	1325	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	77.3518	186	1325	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.3258	214	1325	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	77.253	238	1325	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	77.1035	176	1325	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	77.1025	214	1325	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	76.9245	190	1325	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	76.5848	176	1325	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	76.5115	68	1325	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.5041	104	1325	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.3913	114	1325	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.3375	99	1325	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.1418	98	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:18,430] [INFO] DFAST Taxonomy check result was written to GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:18,430] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:18,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:18,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference/checkm_data
[2024-01-24 14:12:18,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:18,473] [INFO] Task started: CheckM
[2024-01-24 14:12:18,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/checkm_input GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:02,724] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:02,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:02,746] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:02,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:02,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:02,748] [INFO] Task started: Blastn
[2024-01-24 14:13:02,748] [INFO] Running command: blastn -query GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d58b207-b883-4ebe-a786-ee1ed74b5be9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:03,995] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:03,999] [INFO] Selected 19 target genomes.
[2024-01-24 14:13:04,000] [INFO] Target genome list was writen to GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:04,030] [INFO] Task started: fastANI
[2024-01-24 14:13:04,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22ee9b1-7c3e-4de8-b196-daeca0135350/GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna.gz --refList GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:18,021] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:18,036] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:18,037] [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_900142085.1	s__Shimia gijangensis	100.0	1319	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003990645.1	s__Shimia sediminis	79.3176	547	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458215.1	s__Shimia thalassica	78.2353	377	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	96.93	96.93	0.94	0.94	2	-
GCF_900114635.1	s__Shimia aestuarii	78.0574	372	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.8469	282	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	77.8191	303	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005518135.1	s__Shimia litoralis	77.8143	307	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458195.1	s__Ruegeria atlantica	77.6275	222	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.59	95.51	0.84	0.83	3	-
GCF_001458175.1	s__Shimia marina	77.5136	261	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCA_900313015.1	s__OMPR01 sp900313015	77.5045	192	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__OMPR01	95.0	97.69	97.65	0.92	0.91	5	-
GCF_004346865.1	s__Shimia isoporae	77.4836	212	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.2793	242	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	77.2301	241	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743975.1	s__Ruegeria sp017743975	77.2299	205	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003215.1	s__Epibacterium scottomollicae	76.9365	188	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	76.9258	236	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	76.8826	194	1325	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	76.784	185	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.5729	137	1325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:18,038] [INFO] GTDB search result was written to GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:18,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:18,044] [INFO] DFAST_QC result json was written to GCF_900142085.1_IMG-taxon_2700988697_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:18,044] [INFO] DFAST_QC completed!
[2024-01-24 14:13:18,044] [INFO] Total running time: 0h1m31s