[2024-01-24 12:13:54,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:54,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:54,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference
[2024-01-24 12:13:57,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,519] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg27576513-f7df-4048-aca8-02bb782a38da/GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/cds.fna -a GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:11,034] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:11,034] [INFO] Task started: HMMsearch
[2024-01-24 12:14:11,034] [INFO] Running command: hmmsearch --tblout GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference/reference_markers.hmm GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:11,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:11,422] [INFO] Found 6/6 markers.
[2024-01-24 12:14:11,498] [INFO] Query marker FASTA was written to GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:14:11,498] [INFO] Task started: Blastn
[2024-01-24 12:14:11,498] [INFO] Running command: blastn -query GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference/reference_markers.fasta -out GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:12,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:12,509] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:12,510] [INFO] Target genome list was writen to GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:14:12,518] [INFO] Task started: fastANI
[2024-01-24 12:14:12,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg27576513-f7df-4048-aca8-02bb782a38da/GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna.gz --refList GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:26,780] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:26,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:26,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:26,796] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:26,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:26,797] [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
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	100.0	1594	1594	95	conclusive
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	100.0	1594	1594	95	conclusive
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	83.4679	986	1594	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	79.5331	637	1594	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.22	557	1594	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.1532	564	1594	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.128	592	1594	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.2927	452	1594	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2459	424	1594	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1958	402	1594	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.1213	401	1594	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.9781	350	1594	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9759	387	1594	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.8269	382	1594	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	77.8136	448	1594	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6892	353	1594	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.3022	433	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:26,799] [INFO] DFAST Taxonomy check result was written to GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:14:26,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:26,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:26,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference/checkm_data
[2024-01-24 12:14:26,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:26,848] [INFO] Task started: CheckM
[2024-01-24 12:14:26,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/checkm_input GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:15:08,976] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:08,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,000] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:09,000] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:09,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:15:09,001] [INFO] Task started: Blastn
[2024-01-24 12:15:09,001] [INFO] Running command: blastn -query GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ace7320-11bf-4315-a18b-f2001d5464f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:10,734] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:10,739] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:10,739] [INFO] Target genome list was writen to GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:10,748] [INFO] Task started: fastANI
[2024-01-24 12:15:10,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg27576513-f7df-4048-aca8-02bb782a38da/GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna.gz --refList GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:21,923] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:21,935] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:21,935] [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_900116765.1	s__Jannaschia seohaensis	100.0	1594	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003340555.1	s__Jannaschia formosa	83.4498	988	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	79.5158	638	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	79.3483	500	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820245.1	s__Jannaschia sp016820245	79.1917	577	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.1733	562	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113875.1	s__Jannaschia pohangensis	79.121	593	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000877395.1	s__Jannaschia aquimarina	78.9974	529	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.3151	450	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.1707	514	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.9121	355	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	77.8136	448	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.6832	528	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,937] [INFO] GTDB search result was written to GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:21,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:21,943] [INFO] DFAST_QC result json was written to GCF_900116765.1_IMG-taxon_2675903158_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:15:21,943] [INFO] DFAST_QC completed!
[2024-01-24 12:15:21,944] [INFO] Total running time: 0h1m27s