[2024-01-24 14:28:15,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference
[2024-01-24 14:28:17,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgee568d66-ad92-428f-816f-f8bf83519132/GCF_009617595.1_ASM961759v1_genomic.fna.gz | prodigal -d GCF_009617595.1_ASM961759v1_genomic.fna/cds.fna -a GCF_009617595.1_ASM961759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:30,582] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:30,582] [INFO] Task started: HMMsearch
[2024-01-24 14:28:30,582] [INFO] Running command: hmmsearch --tblout GCF_009617595.1_ASM961759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference/reference_markers.hmm GCF_009617595.1_ASM961759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:30,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:30,852] [INFO] Found 6/6 markers.
[2024-01-24 14:28:30,907] [INFO] Query marker FASTA was written to GCF_009617595.1_ASM961759v1_genomic.fna/markers.fasta
[2024-01-24 14:28:30,907] [INFO] Task started: Blastn
[2024-01-24 14:28:30,907] [INFO] Running command: blastn -query GCF_009617595.1_ASM961759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference/reference_markers.fasta -out GCF_009617595.1_ASM961759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:31,739] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:31,742] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:31,742] [INFO] Target genome list was writen to GCF_009617595.1_ASM961759v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:31,843] [INFO] Task started: fastANI
[2024-01-24 14:28:31,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgee568d66-ad92-428f-816f-f8bf83519132/GCF_009617595.1_ASM961759v1_genomic.fna.gz --refList GCF_009617595.1_ASM961759v1_genomic.fna/target_genomes.txt --output GCF_009617595.1_ASM961759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:47,501] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:47,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:47,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:47,518] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:47,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:47,518] [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
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	100.0	1213	1214	95	conclusive
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	80.1197	655	1214	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	78.759	443	1214	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	78.7178	441	1214	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	78.4566	392	1214	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.4159	392	1214	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	78.2142	312	1214	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_002796795.1	1156985	1156985	type	True	78.2048	318	1214	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	78.2016	430	1214	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	78.1877	384	1214	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	78.1661	391	1214	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.8941	385	1214	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.7964	409	1214	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	77.656	230	1214	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	77.6554	257	1214	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.4915	242	1214	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.4684	264	1214	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.7686	187	1214	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.3963	147	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:47,520] [INFO] DFAST Taxonomy check result was written to GCF_009617595.1_ASM961759v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:47,521] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:47,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:47,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference/checkm_data
[2024-01-24 14:28:47,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:47,560] [INFO] Task started: CheckM
[2024-01-24 14:28:47,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009617595.1_ASM961759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009617595.1_ASM961759v1_genomic.fna/checkm_input GCF_009617595.1_ASM961759v1_genomic.fna/checkm_result
[2024-01-24 14:29:25,950] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:25,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:25,967] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:25,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:25,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009617595.1_ASM961759v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:25,968] [INFO] Task started: Blastn
[2024-01-24 14:29:25,969] [INFO] Running command: blastn -query GCF_009617595.1_ASM961759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b37991b-8ddd-4c79-b347-d027c9c88022/dqc_reference/reference_markers_gtdb.fasta -out GCF_009617595.1_ASM961759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:27,224] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:27,227] [INFO] Selected 16 target genomes.
[2024-01-24 14:29:27,227] [INFO] Target genome list was writen to GCF_009617595.1_ASM961759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:27,247] [INFO] Task started: fastANI
[2024-01-24 14:29:27,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgee568d66-ad92-428f-816f-f8bf83519132/GCF_009617595.1_ASM961759v1_genomic.fna.gz --refList GCF_009617595.1_ASM961759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009617595.1_ASM961759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:40,701] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:40,715] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:40,715] [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_009617595.1	s__Epibacterium aquimaris	100.0	1213	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009496005.1	s__Epibacterium litoralis	80.1161	655	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	79.9148	627	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458415.1	s__Epibacterium multivorans	78.7493	444	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001258055.1	s__Phaeobacter italicus	78.4431	394	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	78.2722	402	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900102795.1	s__Epibacterium ulvae	78.2178	312	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000473165.1	s__Leisingera aquimarina	78.1788	401	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001681715.1	s__Epibacterium mobile	78.1601	387	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_000014065.1	s__Epibacterium sp000014065	78.042	372	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	78.0132	384	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	77.9459	433	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.8767	385	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458295.1	s__Ruegeria denitrificans	77.6655	257	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377785.1	s__Ruegeria haliotis	77.6421	231	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	77.4109	273	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:40,717] [INFO] GTDB search result was written to GCF_009617595.1_ASM961759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:40,718] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:40,721] [INFO] DFAST_QC result json was written to GCF_009617595.1_ASM961759v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:40,722] [INFO] DFAST_QC completed!
[2024-01-24 14:29:40,722] [INFO] Total running time: 0h1m25s