[2024-01-24 14:19:02,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference
[2024-01-24 14:19:03,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,778] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,778] [INFO] Running command: gunzip -c /var/lib/cwl/stga279711b-11a6-4621-81ec-72b8872d863a/GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/cds.fna -a GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:15,589] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:15,589] [INFO] Task started: HMMsearch
[2024-01-24 14:19:15,589] [INFO] Running command: hmmsearch --tblout GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference/reference_markers.hmm GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:15,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:15,906] [INFO] Found 6/6 markers.
[2024-01-24 14:19:15,948] [INFO] Query marker FASTA was written to GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:15,948] [INFO] Task started: Blastn
[2024-01-24 14:19:15,948] [INFO] Running command: blastn -query GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference/reference_markers.fasta -out GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:16,740] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:16,743] [INFO] Selected 19 target genomes.
[2024-01-24 14:19:16,744] [INFO] Target genome list was writen to GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:16,757] [INFO] Task started: fastANI
[2024-01-24 14:19:16,757] [INFO] Running command: fastANI --query /var/lib/cwl/stga279711b-11a6-4621-81ec-72b8872d863a/GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna.gz --refList GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:33,264] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:33,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:33,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:33,280] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:33,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:33,281] [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 pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	100.0	1240	1242	95	conclusive
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	88.2038	921	1242	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	80.2141	625	1242	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	79.9478	535	1242	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	79.4934	519	1242	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	79.2631	531	1242	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	79.2447	499	1242	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	79.2272	510	1242	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	79.2099	538	1242	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.7503	489	1242	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.4315	452	1242	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	78.2606	375	1242	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	78.0414	446	1242	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8183	250	1242	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.4044	357	1242	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.2628	317	1242	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2579	288	1242	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.0579	175	1242	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.6619	146	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:33,283] [INFO] DFAST Taxonomy check result was written to GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:19:33,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:33,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:33,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference/checkm_data
[2024-01-24 14:19:33,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:33,323] [INFO] Task started: CheckM
[2024-01-24 14:19:33,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/checkm_input GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:20:12,472] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:12,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:12,493] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:12,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:12,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:20:12,495] [INFO] Task started: Blastn
[2024-01-24 14:20:12,495] [INFO] Running command: blastn -query GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e6cd279-3667-4d54-b633-aa8354ffc1b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:13,844] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:13,847] [INFO] Selected 8 target genomes.
[2024-01-24 14:20:13,847] [INFO] Target genome list was writen to GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:13,853] [INFO] Task started: fastANI
[2024-01-24 14:20:13,853] [INFO] Running command: fastANI --query /var/lib/cwl/stga279711b-11a6-4621-81ec-72b8872d863a/GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna.gz --refList GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:20,921] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:20,929] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:20,929] [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_900106935.1	s__Sulfitobacter pontiacus	100.0	1240	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	conclusive
GCF_900103185.1	s__Sulfitobacter litoralis	88.2188	920	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_006064855.1	s__Sulfitobacter sp006064855	87.2198	852	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	81.3162	686	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	80.9789	700	1242	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	80.6047	541	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	80.2234	624	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	79.1758	537	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:20,931] [INFO] GTDB search result was written to GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:20,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:20,935] [INFO] DFAST_QC result json was written to GCF_900106935.1_IMG-taxon_2622736431_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:20:20,935] [INFO] DFAST_QC completed!
[2024-01-24 14:20:20,935] [INFO] Total running time: 0h1m18s