[2024-01-24 12:36:50,184] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:50,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:50,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference
[2024-01-24 12:36:52,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:52,571] [INFO] Task started: Prodigal
[2024-01-24 12:36:52,571] [INFO] Running command: gunzip -c /var/lib/cwl/stga8568ec4-f656-419f-b184-a7229d6d5be3/GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/cds.fna -a GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:02,863] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:02,863] [INFO] Task started: HMMsearch
[2024-01-24 12:37:02,863] [INFO] Running command: hmmsearch --tblout GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference/reference_markers.hmm GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:03,066] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:03,067] [INFO] Found 6/6 markers.
[2024-01-24 12:37:03,094] [INFO] Query marker FASTA was written to GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:37:03,095] [INFO] Task started: Blastn
[2024-01-24 12:37:03,095] [INFO] Running command: blastn -query GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference/reference_markers.fasta -out GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:03,758] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:03,762] [INFO] Selected 22 target genomes.
[2024-01-24 12:37:03,763] [INFO] Target genome list was writen to GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:37:03,930] [INFO] Task started: fastANI
[2024-01-24 12:37:03,930] [INFO] Running command: fastANI --query /var/lib/cwl/stga8568ec4-f656-419f-b184-a7229d6d5be3/GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna.gz --refList GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:15,873] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:15,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:15,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:15,887] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:15,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:15,887] [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
Halpernia frigidisoli	strain=DSM 26000	GCA_900113805.1	1125876	1125876	type	True	100.0	1000	1001	95	conclusive
Halpernia humi	strain=DSM 21580	GCA_900108025.1	493375	493375	type	True	79.8412	530	1001	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	77.5384	308	1001	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	77.4974	305	1001	95	below_threshold
Frigoriflavimonas asaccharolytica	strain=16F	GCA_013294015.1	2735899	2735899	type	True	77.4851	236	1001	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	77.4692	308	1001	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.2717	233	1001	95	below_threshold
Kaistella treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	77.0634	192	1001	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	76.819	216	1001	95	below_threshold
Epilithonimonas xixisoli	strain=CGMCC 1.12802	GCA_004365655.1	1476462	1476462	type	True	76.7799	153	1001	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	76.7209	190	1001	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	76.6627	209	1001	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	76.6615	214	1001	95	below_threshold
Epilithonimonas hispanica	strain=KCTC 22104	GCA_003385395.1	358687	358687	type	True	76.5657	162	1001	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	76.5536	208	1001	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	76.421	160	1001	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	76.2209	167	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:15,889] [INFO] DFAST Taxonomy check result was written to GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:37:15,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:15,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:15,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference/checkm_data
[2024-01-24 12:37:15,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:15,923] [INFO] Task started: CheckM
[2024-01-24 12:37:15,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/checkm_input GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:37:49,404] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:49,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:49,426] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:49,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:49,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:37:49,427] [INFO] Task started: Blastn
[2024-01-24 12:37:49,427] [INFO] Running command: blastn -query GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg26224bde-dca3-4d88-a42e-b097347638e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:50,462] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:50,465] [INFO] Selected 21 target genomes.
[2024-01-24 12:37:50,465] [INFO] Target genome list was writen to GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:50,518] [INFO] Task started: fastANI
[2024-01-24 12:37:50,519] [INFO] Running command: fastANI --query /var/lib/cwl/stga8568ec4-f656-419f-b184-a7229d6d5be3/GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna.gz --refList GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:01,807] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:01,822] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:01,823] [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_900113805.1	s__Halpernia frigidisoli	100.0	1000	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900108025.1	s__Halpernia humi	79.8165	533	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812865.1	s__Kaistella jeonii	77.4816	305	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
GCF_015679325.1	s__Kaistella gelatinilytica	77.4594	309	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294015.1	s__Halpernia sp013294015	77.448	239	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860585.1	s__Kaistella carnis	77.2596	234	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_015191005.1	s__Kaistella flava	77.2553	285	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415135.1	s__Kaistella sp002415135	77.1066	231	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114045.1	s__Kaistella treverensis	77.0634	192	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.8987	N/A	N/A	N/A	N/A	1	-
GCA_015999765.1	s__Kaistella sp015999765	76.9185	140	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_004365655.1	s__Epilithonimonas xixisoli	76.7767	152	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860505.1	s__Kaistella daneshvariae	76.7209	190	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.86	0.91	0.91	2	-
GCF_907163105.1	s__Cloacibacterium caeni_A	76.711	169	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	76.6812	212	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_000813825.1	s__Chryseobacterium taiwanense	76.6756	149	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898785.1	s__Epilithonimonas sp001898785	76.6118	134	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163125.1	s__Cloacibacterium caeni_B	76.5533	154	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_014779605.1	s__Chryseobacterium sp014779605	76.4609	216	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
GCF_900111495.1	s__Chryseobacterium wanjuense	76.2209	167	1001	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:01,824] [INFO] GTDB search result was written to GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:01,825] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:01,829] [INFO] DFAST_QC result json was written to GCF_900113805.1_IMG-taxon_2684622856_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:38:01,829] [INFO] DFAST_QC completed!
[2024-01-24 12:38:01,829] [INFO] Total running time: 0h1m12s