[2023-03-16 07:34:40,565] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,565] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference
[2023-03-16 07:34:42,231] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,232] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,232] [INFO] Running command: cat /var/lib/cwl/stg97dbcf90-d4da-49bf-929d-f1ada73742ed/OceanDNA-b30080.fa | prodigal -d OceanDNA-b30080/cds.fna -a OceanDNA-b30080/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:34:58,397] [INFO] Task succeeded: Prodigal
[2023-03-16 07:34:58,397] [INFO] Task started: HMMsearch
[2023-03-16 07:34:58,397] [INFO] Running command: hmmsearch --tblout OceanDNA-b30080/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference/reference_markers.hmm OceanDNA-b30080/protein.faa > /dev/null
[2023-03-16 07:34:58,578] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:34:58,579] [INFO] Found 6/6 markers.
[2023-03-16 07:34:58,618] [INFO] Query marker FASTA was written to OceanDNA-b30080/markers.fasta
[2023-03-16 07:34:58,620] [INFO] Task started: Blastn
[2023-03-16 07:34:58,620] [INFO] Running command: blastn -query OceanDNA-b30080/markers.fasta -db /var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference/reference_markers.fasta -out OceanDNA-b30080/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:34:59,431] [INFO] Task succeeded: Blastn
[2023-03-16 07:34:59,431] [INFO] Selected 26 target genomes.
[2023-03-16 07:34:59,432] [INFO] Target genome list was writen to OceanDNA-b30080/target_genomes.txt
[2023-03-16 07:34:59,537] [INFO] Task started: fastANI
[2023-03-16 07:34:59,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg97dbcf90-d4da-49bf-929d-f1ada73742ed/OceanDNA-b30080.fa --refList OceanDNA-b30080/target_genomes.txt --output OceanDNA-b30080/fastani_result.tsv --threads 1
[2023-03-16 07:35:18,845] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:18,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:18,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:18,862] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:18,862] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:35:18,862] [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
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	79.1429	468	874	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.002	434	874	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.9734	437	874	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.8178	405	874	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	78.8004	437	874	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.792	411	874	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.7611	396	874	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	78.6788	401	874	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.6679	384	874	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.6444	406	874	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.5843	453	874	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.5786	403	874	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.5736	462	874	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.5606	455	874	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	78.4601	391	874	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.3711	411	874	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.3579	368	874	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.3252	346	874	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.3089	342	874	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.276	336	874	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.7284	319	874	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.7225	323	874	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.6881	388	874	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.6777	325	874	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.6556	326	874	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.5086	315	874	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:35:18,863] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30080/tc_result.tsv
[2023-03-16 07:35:18,863] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:18,863] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:18,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference/checkm_data
[2023-03-16 07:35:18,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:18,868] [INFO] Task started: CheckM
[2023-03-16 07:35:18,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30080/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30080/checkm_input OceanDNA-b30080/checkm_result
[2023-03-16 07:36:00,984] [INFO] Task succeeded: CheckM
[2023-03-16 07:36:00,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:36:00,986] [INFO] ===== Completeness check finished =====
[2023-03-16 07:36:00,986] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:36:00,986] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30080/markers.fasta)
[2023-03-16 07:36:00,987] [INFO] Task started: Blastn
[2023-03-16 07:36:00,988] [INFO] Running command: blastn -query OceanDNA-b30080/markers.fasta -db /var/lib/cwl/stgd98851f9-b82a-4554-a27c-6f2408248746/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30080/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:36:02,389] [INFO] Task succeeded: Blastn
[2023-03-16 07:36:02,390] [INFO] Selected 29 target genomes.
[2023-03-16 07:36:02,390] [INFO] Target genome list was writen to OceanDNA-b30080/target_genomes_gtdb.txt
[2023-03-16 07:36:03,441] [INFO] Task started: fastANI
[2023-03-16 07:36:03,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg97dbcf90-d4da-49bf-929d-f1ada73742ed/OceanDNA-b30080.fa --refList OceanDNA-b30080/target_genomes_gtdb.txt --output OceanDNA-b30080/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:24,142] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:24,159] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:36:24,159] [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_009762325.1	s__Roseovarius faecimaris	79.1435	468	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	79.0121	433	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.8162	449	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900172255.1	s__Roseovarius halotolerans	78.8127	409	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001441615.1	s__Roseovarius atlanticus	78.7903	438	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.7511	397	874	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_003651245.1	s__Roseovarius spongiae	78.7284	407	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	78.6684	402	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	78.6522	386	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_900142765.1	s__Roseovarius litoreus	78.6303	408	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_009363655.1	s__Roseovarius sp009363655	78.5935	432	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_008728195.1	s__Roseovarius indicus	78.5752	454	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_009363715.1	s__Roseovarius sp009363715	78.5404	405	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	78.4645	390	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_003008555.2	s__Pukyongiella litopenaei	78.435	392	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	78.3618	412	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.3367	345	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.316	372	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072155.1	s__Roseovarius sp002072155	78.3004	409	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.2979	343	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.2875	335	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.2463	362	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389685.1	s__Aquicoccus sp011389685	78.1379	316	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	78.1102	383	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	77.9399	362	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	77.8259	305	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	77.6577	327	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	77.5592	292	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860705.1	s__Salipiger sp018860705	77.3005	292	874	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:24,165] [INFO] GTDB search result was written to OceanDNA-b30080/result_gtdb.tsv
[2023-03-16 07:36:24,176] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:24,186] [INFO] DFAST_QC result json was written to OceanDNA-b30080/dqc_result.json
[2023-03-16 07:36:24,187] [INFO] DFAST_QC completed!
[2023-03-16 07:36:24,187] [INFO] Total running time: 0h1m44s