[2024-01-24 13:57:55,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference
[2024-01-24 13:57:56,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:56,824] [INFO] Task started: Prodigal
[2024-01-24 13:57:56,824] [INFO] Running command: gunzip -c /var/lib/cwl/stgef79a766-a573-4e1a-8cfc-24adf20a32fc/GCF_013377535.1_ASM1337753v1_genomic.fna.gz | prodigal -d GCF_013377535.1_ASM1337753v1_genomic.fna/cds.fna -a GCF_013377535.1_ASM1337753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:10,194] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:10,194] [INFO] Task started: HMMsearch
[2024-01-24 13:58:10,194] [INFO] Running command: hmmsearch --tblout GCF_013377535.1_ASM1337753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference/reference_markers.hmm GCF_013377535.1_ASM1337753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:10,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:10,551] [INFO] Found 6/6 markers.
[2024-01-24 13:58:10,594] [INFO] Query marker FASTA was written to GCF_013377535.1_ASM1337753v1_genomic.fna/markers.fasta
[2024-01-24 13:58:10,595] [INFO] Task started: Blastn
[2024-01-24 13:58:10,595] [INFO] Running command: blastn -query GCF_013377535.1_ASM1337753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference/reference_markers.fasta -out GCF_013377535.1_ASM1337753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:11,510] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:11,513] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:11,513] [INFO] Target genome list was writen to GCF_013377535.1_ASM1337753v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:11,521] [INFO] Task started: fastANI
[2024-01-24 13:58:11,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgef79a766-a573-4e1a-8cfc-24adf20a32fc/GCF_013377535.1_ASM1337753v1_genomic.fna.gz --refList GCF_013377535.1_ASM1337753v1_genomic.fna/target_genomes.txt --output GCF_013377535.1_ASM1337753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:28,024] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:28,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:28,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:28,048] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:28,048] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:28,049] [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
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	100.0	1405	1408	95	conclusive
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	84.6132	914	1408	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	82.2088	819	1408	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.9537	289	1408	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.9246	364	1408	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.9033	427	1408	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.8679	440	1408	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.7997	411	1408	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.6848	395	1408	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.6757	399	1408	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.6093	407	1408	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	77.5805	251	1408	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2849	276	1408	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.2825	299	1408	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.206	302	1408	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.1031	276	1408	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	77.0946	262	1408	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0466	305	1408	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.9377	268	1408	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.5982	226	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:28,050] [INFO] DFAST Taxonomy check result was written to GCF_013377535.1_ASM1337753v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:28,057] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:28,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:28,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference/checkm_data
[2024-01-24 13:58:28,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:28,107] [INFO] Task started: CheckM
[2024-01-24 13:58:28,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377535.1_ASM1337753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377535.1_ASM1337753v1_genomic.fna/checkm_input GCF_013377535.1_ASM1337753v1_genomic.fna/checkm_result
[2024-01-24 13:59:09,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:09,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,218] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:09,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:09,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377535.1_ASM1337753v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:09,219] [INFO] Task started: Blastn
[2024-01-24 13:59:09,219] [INFO] Running command: blastn -query GCF_013377535.1_ASM1337753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg146fd315-0be6-4d16-92e6-1ab47c19c3d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377535.1_ASM1337753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:10,776] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:10,792] [INFO] Selected 18 target genomes.
[2024-01-24 13:59:10,792] [INFO] Target genome list was writen to GCF_013377535.1_ASM1337753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:10,806] [INFO] Task started: fastANI
[2024-01-24 13:59:10,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgef79a766-a573-4e1a-8cfc-24adf20a32fc/GCF_013377535.1_ASM1337753v1_genomic.fna.gz --refList GCF_013377535.1_ASM1337753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377535.1_ASM1337753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:25,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:25,040] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:25,040] [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_013377535.1	s__Donghicola mangrovi	100.0	1405	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	96.45	96.45	0.91	0.91	2	conclusive
GCF_900115865.1	s__Donghicola eburneus	84.6185	915	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	99.41	99.41	0.91	0.91	2	-
GCF_003003355.1	s__Donghicola tyrosinivorans	82.218	818	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	79.0152	453	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	78.2272	462	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002706605.1	s__SAT37 sp002706605	78.142	376	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCF_009857745.1	s__Thalassobius mangrovi	78.0524	415	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.0033	377	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	77.9576	287	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.8453	365	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	77.8393	365	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	77.8311	281	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.699	399	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	77.4036	360	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.3466	349	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	77.2732	300	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	77.2447	263	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313245.1	s__Primorskyibacter marinus	77.0918	261	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,042] [INFO] GTDB search result was written to GCF_013377535.1_ASM1337753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:25,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:25,051] [INFO] DFAST_QC result json was written to GCF_013377535.1_ASM1337753v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:25,051] [INFO] DFAST_QC completed!
[2024-01-24 13:59:25,052] [INFO] Total running time: 0h1m30s