[2024-01-24 15:32:05,509] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,515] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,516] [INFO] DQC Reference Directory: /var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference
[2024-01-24 15:32:06,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,757] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,757] [INFO] Running command: gunzip -c /var/lib/cwl/stge27c8357-2c4e-4705-a9a1-b2c594c0421e/GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/cds.fna -a GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:37,612] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:37,612] [INFO] Task started: HMMsearch
[2024-01-24 15:32:37,613] [INFO] Running command: hmmsearch --tblout GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference/reference_markers.hmm GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:37,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:37,944] [INFO] Found 6/6 markers.
[2024-01-24 15:32:38,001] [INFO] Query marker FASTA was written to GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:32:38,002] [INFO] Task started: Blastn
[2024-01-24 15:32:38,002] [INFO] Running command: blastn -query GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference/reference_markers.fasta -out GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:38,606] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:38,610] [INFO] Selected 16 target genomes.
[2024-01-24 15:32:38,610] [INFO] Target genome list was writen to GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:32:38,640] [INFO] Task started: fastANI
[2024-01-24 15:32:38,640] [INFO] Running command: fastANI --query /var/lib/cwl/stge27c8357-2c4e-4705-a9a1-b2c594c0421e/GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna.gz --refList GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:55,143] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:55,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:55,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:55,154] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:55,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:55,155] [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
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	100.0	2437	2437	95	conclusive
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	81.0726	1061	2437	95	below_threshold
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	80.96	1012	2437	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	78.3934	454	2437	95	below_threshold
Dyadobacter luteus	strain=RS19	GCA_003383615.1	2259619	2259619	type	True	78.1151	324	2437	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	77.4772	317	2437	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	77.4609	321	2437	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	77.3041	213	2437	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	77.2815	216	2437	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	77.1711	288	2437	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	77.1149	307	2437	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	76.8243	191	2437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:55,156] [INFO] DFAST Taxonomy check result was written to GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:32:55,157] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:55,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:55,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference/checkm_data
[2024-01-24 15:32:55,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:55,229] [INFO] Task started: CheckM
[2024-01-24 15:32:55,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/checkm_input GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:34:21,021] [INFO] Task succeeded: CheckM
[2024-01-24 15:34:21,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:34:21,046] [INFO] ===== Completeness check finished =====
[2024-01-24 15:34:21,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:34:21,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:34:21,047] [INFO] Task started: Blastn
[2024-01-24 15:34:21,047] [INFO] Running command: blastn -query GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge59ecc07-8761-416b-9e52-4226f2968be7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:34:21,820] [INFO] Task succeeded: Blastn
[2024-01-24 15:34:21,825] [INFO] Selected 13 target genomes.
[2024-01-24 15:34:21,825] [INFO] Target genome list was writen to GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:34:21,845] [INFO] Task started: fastANI
[2024-01-24 15:34:21,845] [INFO] Running command: fastANI --query /var/lib/cwl/stge27c8357-2c4e-4705-a9a1-b2c594c0421e/GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna.gz --refList GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:34:39,407] [INFO] Task succeeded: fastANI
[2024-01-24 15:34:39,428] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:34:39,428] [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_900108855.1	s__Dyadobacter koreensis	100.0	2437	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015221875.1	s__Dyadobacter sp015221875	81.0726	1061	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	80.9537	1013	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	80.5572	979	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349265.1	s__Dyadobacter psychrotolerans	78.3744	456	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003383615.1	s__Dyadobacter luteus	78.1145	323	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165045.1	s__Dyadobacter sp907165045	77.7526	280	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	77.4772	317	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869225.1	s__Dyadobacter bucti	77.4684	321	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	77.2539	205	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_005860805.1	s__Dyadobacter luticola	77.1982	285	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744695.1	s__Dyadobacter sp017744695	76.8695	226	2437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:34:39,430] [INFO] GTDB search result was written to GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:34:39,431] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:34:39,437] [INFO] DFAST_QC result json was written to GCF_900108855.1_IMG-taxon_2622736476_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:34:39,437] [INFO] DFAST_QC completed!
[2024-01-24 15:34:39,437] [INFO] Total running time: 0h2m34s