[2024-01-24 13:08:57,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:57,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:57,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference
[2024-01-24 13:08:58,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:58,739] [INFO] Task started: Prodigal
[2024-01-24 13:08:58,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c9358fa-2ad9-46d5-8d59-efbf858b6c65/GCF_000812665.2_ASM81266v2_genomic.fna.gz | prodigal -d GCF_000812665.2_ASM81266v2_genomic.fna/cds.fna -a GCF_000812665.2_ASM81266v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:12,630] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:12,630] [INFO] Task started: HMMsearch
[2024-01-24 13:09:12,630] [INFO] Running command: hmmsearch --tblout GCF_000812665.2_ASM81266v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference/reference_markers.hmm GCF_000812665.2_ASM81266v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:12,904] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:12,905] [INFO] Found 6/6 markers.
[2024-01-24 13:09:12,950] [INFO] Query marker FASTA was written to GCF_000812665.2_ASM81266v2_genomic.fna/markers.fasta
[2024-01-24 13:09:12,951] [INFO] Task started: Blastn
[2024-01-24 13:09:12,951] [INFO] Running command: blastn -query GCF_000812665.2_ASM81266v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference/reference_markers.fasta -out GCF_000812665.2_ASM81266v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:13,639] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:13,643] [INFO] Selected 29 target genomes.
[2024-01-24 13:09:13,644] [INFO] Target genome list was writen to GCF_000812665.2_ASM81266v2_genomic.fna/target_genomes.txt
[2024-01-24 13:09:13,687] [INFO] Task started: fastANI
[2024-01-24 13:09:13,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c9358fa-2ad9-46d5-8d59-efbf858b6c65/GCF_000812665.2_ASM81266v2_genomic.fna.gz --refList GCF_000812665.2_ASM81266v2_genomic.fna/target_genomes.txt --output GCF_000812665.2_ASM81266v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:32,176] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:32,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:32,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:32,194] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:32,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:32,195] [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
Falsihalocynthiibacter arcticus	strain=PAMC 20958	GCA_000812665.2	1579316	1579316	type	True	100.0	1457	1458	95	conclusive
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.5647	90	1458	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	77.3018	82	1458	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	77.1233	106	1458	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.0865	93	1458	95	below_threshold
Pacificibacter maritimus	strain=DSM 104731	GCA_003814915.1	762213	762213	type	True	77.0435	85	1458	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	77.0302	103	1458	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.019	91	1458	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.0138	99	1458	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	77.0036	92	1458	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	76.9937	103	1458	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	76.9205	93	1458	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7233	75	1458	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	76.6954	93	1458	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.6317	72	1458	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.5925	109	1458	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.4946	107	1458	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	76.4587	97	1458	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.4521	62	1458	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.1279	85	1458	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	75.9945	65	1458	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	75.8915	67	1458	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.8841	69	1458	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	75.8343	64	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:32,198] [INFO] DFAST Taxonomy check result was written to GCF_000812665.2_ASM81266v2_genomic.fna/tc_result.tsv
[2024-01-24 13:09:32,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:32,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:32,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference/checkm_data
[2024-01-24 13:09:32,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:32,246] [INFO] Task started: CheckM
[2024-01-24 13:09:32,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000812665.2_ASM81266v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000812665.2_ASM81266v2_genomic.fna/checkm_input GCF_000812665.2_ASM81266v2_genomic.fna/checkm_result
[2024-01-24 13:10:14,965] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:14,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:14,985] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:14,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:14,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000812665.2_ASM81266v2_genomic.fna/markers.fasta)
[2024-01-24 13:10:14,987] [INFO] Task started: Blastn
[2024-01-24 13:10:14,987] [INFO] Running command: blastn -query GCF_000812665.2_ASM81266v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c4c0dc-4ae4-44ee-acc0-8572b6c0b5b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000812665.2_ASM81266v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:16,094] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:16,097] [INFO] Selected 28 target genomes.
[2024-01-24 13:10:16,097] [INFO] Target genome list was writen to GCF_000812665.2_ASM81266v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:16,153] [INFO] Task started: fastANI
[2024-01-24 13:10:16,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c9358fa-2ad9-46d5-8d59-efbf858b6c65/GCF_000812665.2_ASM81266v2_genomic.fna.gz --refList GCF_000812665.2_ASM81266v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000812665.2_ASM81266v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:32,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:32,922] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:32,923] [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_000812665.2	s__Halocynthiibacter_B arcticus	100.0	1457	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003352085.1	s__Sulfitobacter sp003352085	78.3537	122	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812685.1	s__Halocynthiibacter namhaensis	77.2863	109	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	77.0755	105	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814915.1	s__Pacificibacter maritimus	77.0451	85	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169395.1	s__HTCC2150 sp000169395	76.9271	93	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HTCC2150	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933395.1	s__Yoonia maritima_A	76.8587	98	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002340515.1	s__Aliiroseovarius sp002340515	76.8498	98	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	76.7513	74	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	76.6954	93	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_900172295.1	s__Roseovarius litorisediminis	76.6899	70	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.6545	90	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	76.5976	91	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143615.1	s__Shimia sp900143615	76.5718	105	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016123485.1	s__Halocynthiibacter sp016123485	76.5655	91	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643735.1	s__Amylibacter cionae	76.5655	91	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109295.1	s__Cognatiyoonia koreensis	76.486	61	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000647975.1	s__Actibacterium mucosum	76.479	96	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003031585.1	s__Halocynthiibacter sp003031585	76.4221	105	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479575.1	s__Pseudophaeobacter sp905479575	76.2218	79	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	76.2065	81	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	76.205	103	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494385.1	s__Profundibacter sp015494385	76.1104	87	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	76.0656	62	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352425.1	s__Profundibacter sp002352425	76.0167	103	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:32,924] [INFO] GTDB search result was written to GCF_000812665.2_ASM81266v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:32,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:32,929] [INFO] DFAST_QC result json was written to GCF_000812665.2_ASM81266v2_genomic.fna/dqc_result.json
[2024-01-24 13:10:32,929] [INFO] DFAST_QC completed!
[2024-01-24 13:10:32,929] [INFO] Total running time: 0h1m35s