[2023-06-28 13:31:58,070] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:58,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:58,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference
[2023-06-28 13:31:59,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:59,307] [INFO] Task started: Prodigal
[2023-06-28 13:31:59,307] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb5d880f-feee-440b-ac38-bf364dbc21b4/GCA_002708925.1_ASM270892v1_genomic.fna.gz | prodigal -d GCA_002708925.1_ASM270892v1_genomic.fna/cds.fna -a GCA_002708925.1_ASM270892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:32:09,376] [INFO] Task succeeded: Prodigal
[2023-06-28 13:32:09,376] [INFO] Task started: HMMsearch
[2023-06-28 13:32:09,376] [INFO] Running command: hmmsearch --tblout GCA_002708925.1_ASM270892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference/reference_markers.hmm GCA_002708925.1_ASM270892v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:32:09,644] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:32:09,646] [INFO] Found 6/6 markers.
[2023-06-28 13:32:09,682] [INFO] Query marker FASTA was written to GCA_002708925.1_ASM270892v1_genomic.fna/markers.fasta
[2023-06-28 13:32:09,682] [INFO] Task started: Blastn
[2023-06-28 13:32:09,682] [INFO] Running command: blastn -query GCA_002708925.1_ASM270892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference/reference_markers.fasta -out GCA_002708925.1_ASM270892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:10,494] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:10,498] [INFO] Selected 23 target genomes.
[2023-06-28 13:32:10,499] [INFO] Target genome list was writen to GCA_002708925.1_ASM270892v1_genomic.fna/target_genomes.txt
[2023-06-28 13:32:10,501] [INFO] Task started: fastANI
[2023-06-28 13:32:10,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5d880f-feee-440b-ac38-bf364dbc21b4/GCA_002708925.1_ASM270892v1_genomic.fna.gz --refList GCA_002708925.1_ASM270892v1_genomic.fna/target_genomes.txt --output GCA_002708925.1_ASM270892v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:32:27,510] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:27,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:32:27,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:32:27,535] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:32:27,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:32:27,535] [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
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.762	547	1107	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	79.2206	506	1107	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	78.5229	444	1107	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.5097	421	1107	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.4967	382	1107	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.4745	419	1107	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.3137	403	1107	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.3063	368	1107	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.2914	371	1107	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.2661	407	1107	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	78.1297	349	1107	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.9987	389	1107	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.8965	357	1107	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.8551	342	1107	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.8374	347	1107	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.8283	323	1107	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.819	359	1107	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	77.5771	280	1107	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.5491	317	1107	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	77.4873	296	1107	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.4366	288	1107	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	77.093	201	1107	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	77.0928	204	1107	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:32:27,537] [INFO] DFAST Taxonomy check result was written to GCA_002708925.1_ASM270892v1_genomic.fna/tc_result.tsv
[2023-06-28 13:32:27,538] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:32:27,538] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:32:27,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference/checkm_data
[2023-06-28 13:32:27,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:32:27,584] [INFO] Task started: CheckM
[2023-06-28 13:32:27,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708925.1_ASM270892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708925.1_ASM270892v1_genomic.fna/checkm_input GCA_002708925.1_ASM270892v1_genomic.fna/checkm_result
[2023-06-28 13:33:02,018] [INFO] Task succeeded: CheckM
[2023-06-28 13:33:02,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:33:02,046] [INFO] ===== Completeness check finished =====
[2023-06-28 13:33:02,046] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:33:02,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708925.1_ASM270892v1_genomic.fna/markers.fasta)
[2023-06-28 13:33:02,047] [INFO] Task started: Blastn
[2023-06-28 13:33:02,047] [INFO] Running command: blastn -query GCA_002708925.1_ASM270892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45c9086-3ebb-4fa4-b151-0f61782c060b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708925.1_ASM270892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:33:03,298] [INFO] Task succeeded: Blastn
[2023-06-28 13:33:03,304] [INFO] Selected 15 target genomes.
[2023-06-28 13:33:03,304] [INFO] Target genome list was writen to GCA_002708925.1_ASM270892v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:33:03,313] [INFO] Task started: fastANI
[2023-06-28 13:33:03,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5d880f-feee-440b-ac38-bf364dbc21b4/GCA_002708925.1_ASM270892v1_genomic.fna.gz --refList GCA_002708925.1_ASM270892v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708925.1_ASM270892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:33:15,374] [INFO] Task succeeded: fastANI
[2023-06-28 13:33:15,392] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:33:15,392] [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
GCA_002708925.1	s__Thalassobius sp002708925	100.0	1093	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	conclusive
GCF_004799325.1	s__Thalassobius vesicularis	82.2811	714	1107	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	80.7694	602	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	80.5676	624	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.7327	550	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	79.2114	507	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	78.5052	446	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	78.4708	420	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_900129345.1	s__Ruegeria intermedia	78.4654	385	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.2458	372	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000744955.1	s__Actibacterium sp000744955	78.2415	403	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.06	335	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_005938215.1	s__Ruegeria sediminis	77.8451	343	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.8374	347	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	77.5907	319	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:33:15,394] [INFO] GTDB search result was written to GCA_002708925.1_ASM270892v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:33:15,395] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:33:15,399] [INFO] DFAST_QC result json was written to GCA_002708925.1_ASM270892v1_genomic.fna/dqc_result.json
[2023-06-28 13:33:15,400] [INFO] DFAST_QC completed!
[2023-06-28 13:33:15,400] [INFO] Total running time: 0h1m17s