[2024-01-24 12:14:33,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,673] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference
[2024-01-24 12:14:34,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dbbbad8-f0cd-40f3-a4e9-06c39a205213/GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/cds.fna -a GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:45,843] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:45,844] [INFO] Task started: HMMsearch
[2024-01-24 12:14:45,844] [INFO] Running command: hmmsearch --tblout GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference/reference_markers.hmm GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:46,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:46,063] [INFO] Found 6/6 markers.
[2024-01-24 12:14:46,088] [INFO] Query marker FASTA was written to GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:14:46,088] [INFO] Task started: Blastn
[2024-01-24 12:14:46,088] [INFO] Running command: blastn -query GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference/reference_markers.fasta -out GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:46,653] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:46,655] [INFO] Selected 23 target genomes.
[2024-01-24 12:14:46,656] [INFO] Target genome list was writen to GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:14:46,661] [INFO] Task started: fastANI
[2024-01-24 12:14:46,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dbbbad8-f0cd-40f3-a4e9-06c39a205213/GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna.gz --refList GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:06,223] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:06,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:06,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:06,232] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:06,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:06,232] [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
Solitalea koreensis	strain=DSM 21342	GCA_900182575.1	543615	543615	type	True	100.0	1099	1100	95	conclusive
Solitalea longa	strain=HR-AV	GCA_002920915.1	2079460	2079460	type	True	78.3204	178	1100	95	below_threshold
Solitalea canadensis	strain=DSM 3403	GCA_000242635.3	995	995	type	True	77.3877	187	1100	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	76.8712	52	1100	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	76.614	55	1100	95	below_threshold
Pedobacter zeae	strain=DSM 100774	GCA_014196715.1	1737356	1737356	type	True	76.5726	61	1100	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	76.5412	58	1100	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	76.5346	54	1100	95	below_threshold
Pedobacter zeae	strain=CGMCC 1.15287	GCA_014641575.1	1737356	1737356	type	True	76.5229	61	1100	95	below_threshold
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	76.4698	53	1100	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	76.4599	73	1100	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	76.1712	52	1100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,233] [INFO] DFAST Taxonomy check result was written to GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:15:06,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:06,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:06,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference/checkm_data
[2024-01-24 12:15:06,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:06,268] [INFO] Task started: CheckM
[2024-01-24 12:15:06,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/checkm_input GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:15:40,654] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:40,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:40,673] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:40,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:40,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:15:40,674] [INFO] Task started: Blastn
[2024-01-24 12:15:40,674] [INFO] Running command: blastn -query GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaba2907-fa89-4a9d-aa96-7d83971aea2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:41,507] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:41,512] [INFO] Selected 27 target genomes.
[2024-01-24 12:15:41,512] [INFO] Target genome list was writen to GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:41,525] [INFO] Task started: fastANI
[2024-01-24 12:15:41,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dbbbad8-f0cd-40f3-a4e9-06c39a205213/GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna.gz --refList GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:04,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:04,748] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:04,749] [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_900182575.1	s__Solitalea koreensis	100.0	1099	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002920915.1	s__Solitalea longa	78.3204	178	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242635.2	s__Solitalea canadensis	77.3593	189	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331685.1	s__Pedobacter sp004331685	76.9184	51	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	-
GCF_900103665.1	s__Pedobacter steynii	76.7636	60	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196715.1	s__Pedobacter zeae	76.6024	60	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014306625.1	s__Pedobacter sp014306625	76.5676	53	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173595.1	s__Pedobacter yonginense	76.5022	52	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613605.1	s__Pedobacter sp018613605	76.4863	57	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_005116455.1	s__Pelobium sp005116455	76.4852	51	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812965.1	s__Pedobacter kyungheensis	76.4831	72	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708265.2	s__Pedobacter sp000708265	76.457	52	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355835.1	s__SYSU-D00535 sp017355835	76.3917	51	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331675.1	s__Pedobacter sp004331675	76.1712	52	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	76.0262	57	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:04,765] [INFO] GTDB search result was written to GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:04,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:04,769] [INFO] DFAST_QC result json was written to GCF_900182575.1_IMG-taxon_2724679707_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:16:04,769] [INFO] DFAST_QC completed!
[2024-01-24 12:16:04,769] [INFO] Total running time: 0h1m31s