[2024-01-25 17:49:35,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:35,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:35,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference
[2024-01-25 17:49:36,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:36,865] [INFO] Task started: Prodigal
[2024-01-25 17:49:36,865] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1fc693a-cd3d-4fc0-986e-dc0c3506cfcf/GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/cds.fna -a GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:49,175] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:49,175] [INFO] Task started: HMMsearch
[2024-01-25 17:49:49,175] [INFO] Running command: hmmsearch --tblout GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference/reference_markers.hmm GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:49,430] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:49,431] [INFO] Found 6/6 markers.
[2024-01-25 17:49:49,466] [INFO] Query marker FASTA was written to GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:49:49,466] [INFO] Task started: Blastn
[2024-01-25 17:49:49,466] [INFO] Running command: blastn -query GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference/reference_markers.fasta -out GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:50,089] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:50,093] [INFO] Selected 15 target genomes.
[2024-01-25 17:49:50,093] [INFO] Target genome list was writen to GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:49:50,122] [INFO] Task started: fastANI
[2024-01-25 17:49:50,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1fc693a-cd3d-4fc0-986e-dc0c3506cfcf/GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna.gz --refList GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:02,518] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:02,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:02,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:02,529] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:50:02,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:02,530] [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
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	100.0	1373	1374	95	conclusive
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	89.8363	1102	1374	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.4859	763	1374	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.4213	766	1374	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	80.3209	771	1374	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	80.2294	748	1374	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	80.0723	685	1374	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	80.046	751	1374	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	79.6877	628	1374	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	78.9991	573	1374	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.6591	103	1374	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.564	96	1374	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.3128	50	1374	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.0784	95	1374	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	75.6141	54	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:02,531] [INFO] DFAST Taxonomy check result was written to GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:50:02,532] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:02,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:02,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference/checkm_data
[2024-01-25 17:50:02,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:02,573] [INFO] Task started: CheckM
[2024-01-25 17:50:02,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/checkm_input GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:50:39,657] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:39,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:39,675] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:39,675] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:39,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:50:39,676] [INFO] Task started: Blastn
[2024-01-25 17:50:39,676] [INFO] Running command: blastn -query GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg746393f7-2136-4af0-9157-dcdeb6dbffe0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:40,612] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:40,615] [INFO] Selected 11 target genomes.
[2024-01-25 17:50:40,615] [INFO] Target genome list was writen to GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:40,637] [INFO] Task started: fastANI
[2024-01-25 17:50:40,637] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1fc693a-cd3d-4fc0-986e-dc0c3506cfcf/GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna.gz --refList GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:50,900] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:50,908] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:50,908] [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_900109345.1	s__Maribacter orientalis	100.0	1373	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167935.1	s__Maribacter arcticus	89.8398	1102	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	80.5816	788	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.565	750	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900112245.1	s__Maribacter stanieri	80.4859	763	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.435	763	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142175.1	s__Maribacter aquivivus	80.2449	747	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	80.0726	686	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	80.0619	737	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	80.0305	752	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188415.1	s__Maribacter sedimenticola	79.0151	571	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:50,909] [INFO] GTDB search result was written to GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:50,910] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:50,914] [INFO] DFAST_QC result json was written to GCF_900109345.1_IMG-taxon_2622736438_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:50:50,914] [INFO] DFAST_QC completed!
[2024-01-25 17:50:50,914] [INFO] Total running time: 0h1m15s