[2024-01-24 14:14:06,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:06,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:06,201] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference
[2024-01-24 14:14:07,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,488] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgae023022-a9b1-491b-8a8a-8571c775f6d3/GCF_014196805.1_ASM1419680v1_genomic.fna.gz | prodigal -d GCF_014196805.1_ASM1419680v1_genomic.fna/cds.fna -a GCF_014196805.1_ASM1419680v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:20,755] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:20,756] [INFO] Task started: HMMsearch
[2024-01-24 14:14:20,756] [INFO] Running command: hmmsearch --tblout GCF_014196805.1_ASM1419680v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference/reference_markers.hmm GCF_014196805.1_ASM1419680v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:21,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:21,035] [INFO] Found 6/6 markers.
[2024-01-24 14:14:21,070] [INFO] Query marker FASTA was written to GCF_014196805.1_ASM1419680v1_genomic.fna/markers.fasta
[2024-01-24 14:14:21,071] [INFO] Task started: Blastn
[2024-01-24 14:14:21,071] [INFO] Running command: blastn -query GCF_014196805.1_ASM1419680v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference/reference_markers.fasta -out GCF_014196805.1_ASM1419680v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:21,832] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:21,836] [INFO] Selected 20 target genomes.
[2024-01-24 14:14:21,837] [INFO] Target genome list was writen to GCF_014196805.1_ASM1419680v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:21,853] [INFO] Task started: fastANI
[2024-01-24 14:14:21,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgae023022-a9b1-491b-8a8a-8571c775f6d3/GCF_014196805.1_ASM1419680v1_genomic.fna.gz --refList GCF_014196805.1_ASM1419680v1_genomic.fna/target_genomes.txt --output GCF_014196805.1_ASM1419680v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:36,111] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:36,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:36,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:36,132] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:36,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:36,133] [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
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	100.0	1258	1259	95	conclusive
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	79.3079	472	1259	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	79.225	479	1259	95	below_threshold
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	77.9949	379	1259	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.8882	291	1259	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.8238	293	1259	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.6619	331	1259	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.6369	331	1259	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.6015	250	1259	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.4285	308	1259	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.4155	275	1259	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.968	139	1259	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.744	104	1259	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.6213	68	1259	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.619	125	1259	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	76.5095	160	1259	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	76.4473	133	1259	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.3369	136	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:36,135] [INFO] DFAST Taxonomy check result was written to GCF_014196805.1_ASM1419680v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:36,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:36,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:36,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference/checkm_data
[2024-01-24 14:14:36,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:36,175] [INFO] Task started: CheckM
[2024-01-24 14:14:36,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196805.1_ASM1419680v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196805.1_ASM1419680v1_genomic.fna/checkm_input GCF_014196805.1_ASM1419680v1_genomic.fna/checkm_result
[2024-01-24 14:15:16,727] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:16,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:16,753] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:16,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:16,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196805.1_ASM1419680v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:16,754] [INFO] Task started: Blastn
[2024-01-24 14:15:16,754] [INFO] Running command: blastn -query GCF_014196805.1_ASM1419680v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb07b7ea-89af-4379-963c-755b6f926e1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196805.1_ASM1419680v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:18,243] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:18,246] [INFO] Selected 21 target genomes.
[2024-01-24 14:15:18,246] [INFO] Target genome list was writen to GCF_014196805.1_ASM1419680v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:18,269] [INFO] Task started: fastANI
[2024-01-24 14:15:18,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgae023022-a9b1-491b-8a8a-8571c775f6d3/GCF_014196805.1_ASM1419680v1_genomic.fna.gz --refList GCF_014196805.1_ASM1419680v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196805.1_ASM1419680v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:34,545] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:34,570] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:34,571] [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_014196805.1	s__Sulfitobacter undariae	100.0	1258	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000622405.1	s__Sulfitobacter donghicola	79.2346	478	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003610455.1	s__Sulfitobacter guttiformis	77.9887	378	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013282155.1	s__Sulfitobacter sp013282155	77.9635	357	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_900103185.1	s__Sulfitobacter litoralis	77.8986	291	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.8222	293	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	77.7082	309	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.6532	328	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.4433	241	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900116285.1	s__Sulfitobacter marinus	77.4285	308	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.4251	276	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156335.1	s__Sulfitobacter sp000156335	77.4201	311	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172095.1	s__Sulfitobacter indolifex	77.3937	281	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.3221	285	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.2777	331	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.2076	234	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	76.6685	196	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377535.1	s__Donghicola mangrovi	76.4473	133	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	96.45	96.45	0.91	0.91	2	-
GCA_002401945.1	s__Parasedimentitalea sp002401945	76.3741	146	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	76.3369	136	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	76.1942	126	1259	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:34,572] [INFO] GTDB search result was written to GCF_014196805.1_ASM1419680v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:34,573] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:34,577] [INFO] DFAST_QC result json was written to GCF_014196805.1_ASM1419680v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:34,577] [INFO] DFAST_QC completed!
[2024-01-24 14:15:34,577] [INFO] Total running time: 0h1m28s