[2024-01-24 12:46:56,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:56,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:56,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference
[2024-01-24 12:46:58,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:58,006] [INFO] Task started: Prodigal
[2024-01-24 12:46:58,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg23b96e9b-b66c-43aa-a08b-13bd456cba4a/GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/cds.fna -a GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:09,019] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:09,019] [INFO] Task started: HMMsearch
[2024-01-24 12:47:09,019] [INFO] Running command: hmmsearch --tblout GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference/reference_markers.hmm GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:09,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:09,280] [INFO] Found 6/6 markers.
[2024-01-24 12:47:09,318] [INFO] Query marker FASTA was written to GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:09,319] [INFO] Task started: Blastn
[2024-01-24 12:47:09,319] [INFO] Running command: blastn -query GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference/reference_markers.fasta -out GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:10,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:10,194] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:10,194] [INFO] Target genome list was writen to GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:10,211] [INFO] Task started: fastANI
[2024-01-24 12:47:10,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b96e9b-b66c-43aa-a08b-13bd456cba4a/GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna.gz --refList GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:24,805] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:24,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:24,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:24,824] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:24,824] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:47:24,825] [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
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	100.0	1169	1174	95	inconclusive
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	96.335	1038	1174	95	inconclusive
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	79.8299	534	1174	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	79.8103	541	1174	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.6937	569	1174	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	79.6238	567	1174	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.9655	573	1174	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.9338	471	1174	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	78.8826	516	1174	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.7857	469	1174	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7214	451	1174	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.6128	427	1174	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.5998	429	1174	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.4744	439	1174	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.2153	432	1174	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.1996	413	1174	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.9083	344	1174	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.472	297	1174	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	77.4279	290	1174	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.3682	298	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:24,829] [INFO] DFAST Taxonomy check result was written to GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:24,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:24,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:24,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference/checkm_data
[2024-01-24 12:47:24,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:24,873] [INFO] Task started: CheckM
[2024-01-24 12:47:24,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/checkm_input GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:48:02,106] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:02,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:02,127] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:02,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:02,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:48:02,128] [INFO] Task started: Blastn
[2024-01-24 12:48:02,129] [INFO] Running command: blastn -query GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79c1ece9-a13b-4627-b621-7a533aa508cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:03,673] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:03,677] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:03,677] [INFO] Target genome list was writen to GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:03,690] [INFO] Task started: fastANI
[2024-01-24 12:48:03,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b96e9b-b66c-43aa-a08b-13bd456cba4a/GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna.gz --refList GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:15,601] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:15,621] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:15,622] [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_900141995.1	s__Palleronia salina	100.0	1170	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110115.1	s__Palleronia pelagia	96.3377	1039	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	82.9724	793	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	79.901	641	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	79.8208	535	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000743715.1	s__Palleronia rufa	79.6894	568	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358695.1	s__Palleronia sp004358695	79.5915	571	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302445.1	s__Palleronia abyssalis	79.5345	562	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	79.4724	535	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.4641	530	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	79.1529	484	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.9377	470	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	78.6644	472	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003008555.2	s__Pukyongiella litopenaei	78.5537	473	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.3885	296	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:15,623] [INFO] GTDB search result was written to GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:15,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:15,627] [INFO] DFAST_QC result json was written to GCF_900141995.1_IMG-taxon_2619618996_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:48:15,628] [INFO] DFAST_QC completed!
[2024-01-24 12:48:15,628] [INFO] Total running time: 0h1m19s