[2024-01-24 13:57:43,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference
[2024-01-24 13:57:45,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,029] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg7063ea7e-df6f-4250-a3f6-12b9bb0f2bdb/GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/cds.fna -a GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:00,659] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:00,659] [INFO] Task started: HMMsearch
[2024-01-24 13:58:00,659] [INFO] Running command: hmmsearch --tblout GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference/reference_markers.hmm GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:00,955] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:00,957] [INFO] Found 6/6 markers.
[2024-01-24 13:58:00,998] [INFO] Query marker FASTA was written to GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:00,998] [INFO] Task started: Blastn
[2024-01-24 13:58:00,998] [INFO] Running command: blastn -query GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference/reference_markers.fasta -out GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:01,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:01,675] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:01,676] [INFO] Target genome list was writen to GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:01,712] [INFO] Task started: fastANI
[2024-01-24 13:58:01,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg7063ea7e-df6f-4250-a3f6-12b9bb0f2bdb/GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna.gz --refList GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:16,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:16,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:16,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:16,800] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:16,800] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:16,800] [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 marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	79.7653	651	1481	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	79.7606	643	1481	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	79.2335	529	1481	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	78.5168	406	1481	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.8521	202	1481	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.8077	215	1481	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.7112	236	1481	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.6044	315	1481	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	77.5992	336	1481	95	below_threshold
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	77.5791	244	1481	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	77.4856	212	1481	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.3628	256	1481	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	77.188	198	1481	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	77.1224	154	1481	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.9741	192	1481	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.6651	118	1481	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	76.4318	130	1481	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	76.4257	103	1481	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	76.0961	71	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:16,802] [INFO] DFAST Taxonomy check result was written to GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:16,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:16,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:16,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference/checkm_data
[2024-01-24 13:58:16,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:16,847] [INFO] Task started: CheckM
[2024-01-24 13:58:16,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/checkm_input GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:06,832] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:06,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,856] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:06,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:06,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:06,857] [INFO] Task started: Blastn
[2024-01-24 13:59:06,857] [INFO] Running command: blastn -query GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg973d1957-1f92-4d70-adc1-749f57f4e80d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,829] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:07,829] [INFO] Target genome list was writen to GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:07,877] [INFO] Task started: fastANI
[2024-01-24 13:59:07,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg7063ea7e-df6f-4250-a3f6-12b9bb0f2bdb/GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna.gz --refList GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:17,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:17,144] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:17,144] [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
GCA_900537125.1	s__Shimia sp900537125	85.9536	1130	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872815.1	s__Shimia sp014872815	83.716	996	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	97.10	97.10	0.91	0.91	2	-
GCF_017743735.1	s__Shimia sp017743735	79.8619	716	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_001458175.1	s__Shimia marina	79.7623	651	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_017744095.1	s__Shimia sp017744095	79.6051	635	1481	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	78.7933	516	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143615.1	s__Shimia sp900143615	77.9782	416	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	77.6042	315	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900142085.1	s__Shimia gijangensis	77.2985	284	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	76.56	137	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020355.1	s__Thioclava sediminum	76.4125	105	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,147] [INFO] GTDB search result was written to GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:17,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:17,158] [INFO] DFAST_QC result json was written to GCF_900182745.1_IMG-taxon_2724679805_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:17,158] [INFO] DFAST_QC completed!
[2024-01-24 13:59:17,159] [INFO] Total running time: 0h1m33s