[2024-01-25 19:01:50,736] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:50,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:50,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference
[2024-01-25 19:01:51,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:51,891] [INFO] Task started: Prodigal
[2024-01-25 19:01:51,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg32472dd9-c347-4ca4-91f6-8a2e31726088/GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/cds.fna -a GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:00,661] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:00,662] [INFO] Task started: HMMsearch
[2024-01-25 19:02:00,662] [INFO] Running command: hmmsearch --tblout GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference/reference_markers.hmm GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:00,943] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:00,944] [INFO] Found 6/6 markers.
[2024-01-25 19:02:00,973] [INFO] Query marker FASTA was written to GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:02:00,973] [INFO] Task started: Blastn
[2024-01-25 19:02:00,974] [INFO] Running command: blastn -query GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference/reference_markers.fasta -out GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:01,641] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:01,644] [INFO] Selected 15 target genomes.
[2024-01-25 19:02:01,644] [INFO] Target genome list was writen to GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:02:01,654] [INFO] Task started: fastANI
[2024-01-25 19:02:01,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg32472dd9-c347-4ca4-91f6-8a2e31726088/GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna.gz --refList GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:11,831] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:11,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:11,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:11,841] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:11,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:11,842] [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
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	100.0	1157	1158	95	conclusive
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	83.7842	793	1158	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	80.5803	648	1158	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	79.9133	519	1158	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	79.2227	534	1158	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	78.8178	498	1158	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.8039	499	1158	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	78.7736	503	1158	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	78.7096	491	1158	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	78.2637	416	1158	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.2566	194	1158	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.1313	126	1158	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.8896	181	1158	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.8588	98	1158	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2419	149	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:11,843] [INFO] DFAST Taxonomy check result was written to GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:02:11,844] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:11,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:11,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference/checkm_data
[2024-01-25 19:02:11,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:11,882] [INFO] Task started: CheckM
[2024-01-25 19:02:11,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/checkm_input GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:02:39,824] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:39,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:39,839] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:39,839] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:39,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:02:39,840] [INFO] Task started: Blastn
[2024-01-25 19:02:39,840] [INFO] Running command: blastn -query GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg76989726-fa1f-45f6-a373-ebc472351910/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:40,805] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:40,807] [INFO] Selected 8 target genomes.
[2024-01-25 19:02:40,807] [INFO] Target genome list was writen to GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:40,829] [INFO] Task started: fastANI
[2024-01-25 19:02:40,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg32472dd9-c347-4ca4-91f6-8a2e31726088/GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna.gz --refList GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:47,875] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:47,881] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:47,881] [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_900114005.1	s__Olleya namhaensis	100.0	1157	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	conclusive
GCF_002831645.1	s__Olleya sp002831645	86.2536	932	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004843725.1	s__Olleya sp004843725	85.3423	909	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	83.7941	810	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_000518485.1	s__Olleya marilimosa	83.7776	794	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_016785945.1	s__Olleya sediminilitoris	82.0407	760	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	78.7737	503	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_008086175.1	s__Bizionia saleffrena	77.8979	266	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	99.23	99.23	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:47,882] [INFO] GTDB search result was written to GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:47,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:47,885] [INFO] DFAST_QC result json was written to GCF_900114005.1_IMG-taxon_2693429874_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:02:47,885] [INFO] DFAST_QC completed!
[2024-01-25 19:02:47,885] [INFO] Total running time: 0h0m57s