[2024-01-24 12:36:58,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference
[2024-01-24 12:36:59,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,774] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg12a6fab6-17ec-4506-91c7-2e67b600f326/GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/cds.fna -a GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:36,129] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:36,129] [INFO] Task started: HMMsearch
[2024-01-24 12:37:36,129] [INFO] Running command: hmmsearch --tblout GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference/reference_markers.hmm GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:36,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:36,564] [INFO] Found 6/6 markers.
[2024-01-24 12:37:36,637] [INFO] Query marker FASTA was written to GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:37:36,638] [INFO] Task started: Blastn
[2024-01-24 12:37:36,638] [INFO] Running command: blastn -query GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference/reference_markers.fasta -out GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:37,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:37,305] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:37,305] [INFO] Target genome list was writen to GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:37:37,336] [INFO] Task started: fastANI
[2024-01-24 12:37:37,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a6fab6-17ec-4506-91c7-2e67b600f326/GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna.gz --refList GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:02,077] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:02,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:02,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:02,091] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:02,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:02,091] [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 psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	100.0	2226	2229	95	conclusive
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	83.2723	1419	2229	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	79.6892	632	2229	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	79.2928	675	2229	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	79.0777	433	2229	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	78.7373	651	2229	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	78.5575	691	2229	95	below_threshold
Dyadobacter arcticus	strain=DSM 102865	GCA_011762185.1	1078754	1078754	type	True	78.2899	568	2229	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	78.0169	573	2229	95	below_threshold
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	77.9435	565	2229	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	77.8924	564	2229	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	77.8523	612	2229	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	77.7444	424	2229	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	77.5736	610	2229	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	77.5654	607	2229	95	below_threshold
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	77.5013	359	2229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:02,093] [INFO] DFAST Taxonomy check result was written to GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:38:02,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:02,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:02,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference/checkm_data
[2024-01-24 12:38:02,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:02,161] [INFO] Task started: CheckM
[2024-01-24 12:38:02,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/checkm_input GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:39:35,357] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:35,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:35,384] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:35,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:35,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:39:35,385] [INFO] Task started: Blastn
[2024-01-24 12:39:35,385] [INFO] Running command: blastn -query GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg111e9850-ca94-4684-b743-9e35442e6106/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:36,139] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:36,142] [INFO] Selected 18 target genomes.
[2024-01-24 12:39:36,143] [INFO] Target genome list was writen to GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:36,857] [INFO] Task started: fastANI
[2024-01-24 12:39:36,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a6fab6-17ec-4506-91c7-2e67b600f326/GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna.gz --refList GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:01,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:01,792] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:01,792] [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_900167945.1	s__Dyadobacter psychrophilus	100.0	2226	2229	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_000428845.1	s__Dyadobacter alkalitolerans	83.2638	1421	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860765.1	s__Dyadobacter sediminis	79.5799	645	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869225.1	s__Dyadobacter bucti	79.2931	675	2229	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	79.0777	433	2229	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	78.7488	657	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149045.1	s__Dyadobacter flavalbus	78.7454	650	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860805.1	s__Dyadobacter luticola	78.5651	690	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	78.3098	588	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762185.1	s__Dyadobacter arcticus	78.285	570	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	78.2206	617	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701505.1	s__Dyadobacter crusticola	78.0157	575	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023125.1	s__Dyadobacter fermentans	77.894	563	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	77.8577	612	2229	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	77.8272	608	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_900109045.1	s__Dyadobacter sp900109045	77.7009	647	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	77.5693	610	2229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005280585.1	s__Dyadobacter frigoris	77.5012	359	2229	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 12:40:01,794] [INFO] GTDB search result was written to GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:01,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:01,799] [INFO] DFAST_QC result json was written to GCF_900167945.1_IMG-taxon_2595698219_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:40:01,799] [INFO] DFAST_QC completed!
[2024-01-24 12:40:01,799] [INFO] Total running time: 0h3m3s