[2024-01-24 13:57:44,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference
[2024-01-24 13:57:45,516] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,517] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,517] [INFO] Running command: gunzip -c /var/lib/cwl/stg971152b0-54b8-48d3-8041-cbddaf3e3afe/GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/cds.fna -a GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:01,485] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:01,486] [INFO] Task started: HMMsearch
[2024-01-24 13:58:01,486] [INFO] Running command: hmmsearch --tblout GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference/reference_markers.hmm GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:01,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:01,764] [INFO] Found 6/6 markers.
[2024-01-24 13:58:01,800] [INFO] Query marker FASTA was written to GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:01,800] [INFO] Task started: Blastn
[2024-01-24 13:58:01,801] [INFO] Running command: blastn -query GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference/reference_markers.fasta -out GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:02,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:02,527] [INFO] Selected 28 target genomes.
[2024-01-24 13:58:02,527] [INFO] Target genome list was writen to GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:02,597] [INFO] Task started: fastANI
[2024-01-24 13:58:02,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg971152b0-54b8-48d3-8041-cbddaf3e3afe/GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna.gz --refList GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:21,631] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:21,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:21,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:21,652] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:21,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:21,652] [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
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	100.0	1386	1388	95	conclusive
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	77.2677	112	1388	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.2462	111	1388	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.9863	76	1388	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.9474	112	1388	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	76.9327	184	1388	95	below_threshold
Imtechella halotolerans	strain=K1	GCA_000260835.1	1165090	1165090	type	True	76.82	82	1388	95	below_threshold
Zhouia amylolytica	strain=CGMCC 1.6114	GCA_900116365.1	376730	376730	type	True	76.7974	95	1388	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.62	134	1388	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.5985	115	1388	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	76.5722	119	1388	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	76.56	124	1388	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.5358	85	1388	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.5135	86	1388	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	76.5012	117	1388	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.4848	89	1388	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	76.4689	102	1388	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	76.4402	123	1388	95	below_threshold
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	76.3801	53	1388	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.3647	115	1388	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	76.3215	103	1388	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.3193	100	1388	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	76.3098	63	1388	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	76.3052	81	1388	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.2835	119	1388	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.2785	73	1388	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	75.9857	80	1388	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	75.9249	96	1388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,654] [INFO] DFAST Taxonomy check result was written to GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:21,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:21,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:21,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference/checkm_data
[2024-01-24 13:58:21,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:21,705] [INFO] Task started: CheckM
[2024-01-24 13:58:21,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/checkm_input GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:11,781] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:11,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,800] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:11,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:11,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:11,801] [INFO] Task started: Blastn
[2024-01-24 13:59:11,802] [INFO] Running command: blastn -query GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b78520f-32ca-4f71-b2a8-937d83213622/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:12,769] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:12,774] [INFO] Selected 25 target genomes.
[2024-01-24 13:59:12,774] [INFO] Target genome list was writen to GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:13,265] [INFO] Task started: fastANI
[2024-01-24 13:59:13,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg971152b0-54b8-48d3-8041-cbddaf3e3afe/GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna.gz --refList GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:28,719] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:28,746] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:28,747] [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_900116665.1	s__Pustulibacterium marinum	100.0	1386	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003337215.1	s__Oceanihabitans sediminis	77.2453	111	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008033385.1	s__Algibacter pacificus	76.9688	111	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	76.939	108	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260115.1	s__Joostella marina	76.9327	184	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391805.1	s__Galbibacter_A sp013391805	76.9227	103	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260835.1	s__Imtechella halotolerans	76.7903	83	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Imtechella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	76.6778	121	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_900102165.1	s__Cellulophaga baltica	76.6163	114	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_001005305.1	s__Kordia zhangzhouensis	76.5785	124	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	76.4905	120	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.4861	132	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014397005.1	s__Kordia aestuariivivens	76.4835	118	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352465.1	s__Kordia sp003352465	76.4833	122	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.4167	100	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215095.1	s__DT-34 sp013215095	76.3792	71	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	76.3269	80	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.3218	131	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293845.1	s__Flavobacterium tibetense	76.3215	103	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744255.1	s__Maribacter_B sp016744255	76.2013	98	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	76.0691	70	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	75.9867	80	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296885.1	s__Flavobacterium sp002296885	75.6917	52	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744415.1	s__Urechidicola sp016744415	75.6436	83	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479815.1	s__Psychroserpens sp905479815	75.555	75	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:28,748] [INFO] GTDB search result was written to GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:28,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:28,754] [INFO] DFAST_QC result json was written to GCF_900116665.1_IMG-taxon_2663762752_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:28,754] [INFO] DFAST_QC completed!
[2024-01-24 13:59:28,754] [INFO] Total running time: 0h1m44s