[2024-01-25 17:53:05,673] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:05,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:05,674] [INFO] DQC Reference Directory: /var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference
[2024-01-25 17:53:06,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:06,826] [INFO] Task started: Prodigal
[2024-01-25 17:53:06,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg12ef0a5f-8da8-4d2a-b863-6ff68deb628d/GCF_014640175.1_ASM1464017v1_genomic.fna.gz | prodigal -d GCF_014640175.1_ASM1464017v1_genomic.fna/cds.fna -a GCF_014640175.1_ASM1464017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:14,479] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:14,479] [INFO] Task started: HMMsearch
[2024-01-25 17:53:14,479] [INFO] Running command: hmmsearch --tblout GCF_014640175.1_ASM1464017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference/reference_markers.hmm GCF_014640175.1_ASM1464017v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:14,689] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:14,691] [INFO] Found 6/6 markers.
[2024-01-25 17:53:14,717] [INFO] Query marker FASTA was written to GCF_014640175.1_ASM1464017v1_genomic.fna/markers.fasta
[2024-01-25 17:53:14,717] [INFO] Task started: Blastn
[2024-01-25 17:53:14,717] [INFO] Running command: blastn -query GCF_014640175.1_ASM1464017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference/reference_markers.fasta -out GCF_014640175.1_ASM1464017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:15,315] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:15,318] [INFO] Selected 23 target genomes.
[2024-01-25 17:53:15,318] [INFO] Target genome list was writen to GCF_014640175.1_ASM1464017v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:15,342] [INFO] Task started: fastANI
[2024-01-25 17:53:15,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ef0a5f-8da8-4d2a-b863-6ff68deb628d/GCF_014640175.1_ASM1464017v1_genomic.fna.gz --refList GCF_014640175.1_ASM1464017v1_genomic.fna/target_genomes.txt --output GCF_014640175.1_ASM1464017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:28,575] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:28,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:28,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:28,588] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:28,588] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:28,588] [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
Psychroflexus salis	strain=CGMCC 1.12925	GCA_014640175.1	1526574	1526574	type	True	100.0	941	941	95	conclusive
Psychroflexus planctonicus	strain=CGMCC 1.12931	GCA_014640195.1	1526575	1526575	type	True	80.2996	581	941	95	below_threshold
Psychroflexus maritimus	strain=C1	GCA_011089875.1	2714865	2714865	type	True	77.5767	158	941	95	below_threshold
Psychroflexus salarius	strain=DSM 25661	GCA_900129035.1	1155689	1155689	type	True	77.0844	149	941	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.753	117	941	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	76.4525	59	941	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	76.4043	115	941	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	76.3489	114	941	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.3383	100	941	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.312	62	941	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2691	77	941	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	76.2411	83	941	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	76.2268	56	941	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	76.2199	84	941	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.2126	73	941	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	76.1748	81	941	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	75.993	55	941	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	75.9754	81	941	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	75.8939	69	941	95	below_threshold
Flavobacterium lacus	strain=CGMCC 1.12504	GCA_003268815.1	1353778	1353778	type	True	75.8777	72	941	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	75.786	57	941	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.7138	63	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:28,590] [INFO] DFAST Taxonomy check result was written to GCF_014640175.1_ASM1464017v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:28,590] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:28,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:28,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference/checkm_data
[2024-01-25 17:53:28,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:28,620] [INFO] Task started: CheckM
[2024-01-25 17:53:28,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640175.1_ASM1464017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640175.1_ASM1464017v1_genomic.fna/checkm_input GCF_014640175.1_ASM1464017v1_genomic.fna/checkm_result
[2024-01-25 17:53:54,570] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:54,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:54,590] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:54,590] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:54,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640175.1_ASM1464017v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:54,590] [INFO] Task started: Blastn
[2024-01-25 17:53:54,590] [INFO] Running command: blastn -query GCF_014640175.1_ASM1464017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga240d81d-e87a-43cd-91b1-bc46f8a4af51/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640175.1_ASM1464017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:55,519] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:55,521] [INFO] Selected 20 target genomes.
[2024-01-25 17:53:55,522] [INFO] Target genome list was writen to GCF_014640175.1_ASM1464017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:55,537] [INFO] Task started: fastANI
[2024-01-25 17:53:55,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ef0a5f-8da8-4d2a-b863-6ff68deb628d/GCF_014640175.1_ASM1464017v1_genomic.fna.gz --refList GCF_014640175.1_ASM1464017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640175.1_ASM1464017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:07,443] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:07,455] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:07,455] [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_014640175.1	s__Psychroflexus salis	100.0	941	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014640195.1	s__Psychroflexus planctonicus	80.3309	578	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089875.1	s__Psychroflexus maritimus	77.5574	159	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311165.1	s__Psychroflexus sp017311165	76.9358	154	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007116535.1	s__Psychroflexus sp007116535	76.7706	69	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564185.1	s__Psychroflexus sp003564185	76.6296	133	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003931895.1	s__Psychroflexus sp003931895	76.5492	104	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	76.4525	59	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	76.4043	115	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCF_018080005.1	s__Psychroflexus sp018080005	76.3401	89	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006546625.1	s__Mesonia sp006546625	76.3383	100	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.2691	77	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129445.1	s__Salegentibacter echinorum	76.2268	56	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	76.2216	90	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.1856	103	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260115.1	s__Joostella marina	76.1748	81	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	75.9754	81	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	75.8983	78	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268815.1	s__Flavobacterium lacus	75.8777	72	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638005.1	s__Flavobacterium orientale	75.786	57	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:07,457] [INFO] GTDB search result was written to GCF_014640175.1_ASM1464017v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:07,458] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:07,463] [INFO] DFAST_QC result json was written to GCF_014640175.1_ASM1464017v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:07,463] [INFO] DFAST_QC completed!
[2024-01-25 17:54:07,463] [INFO] Total running time: 0h1m2s