[2023-03-16 07:28:29,977] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,977] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference
[2023-03-16 07:28:31,076] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,076] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,076] [INFO] Running command: cat /var/lib/cwl/stg67e7fb3b-26a1-4fce-beb2-e739a94dda17/OceanDNA-b30079.fa | prodigal -d OceanDNA-b30079/cds.fna -a OceanDNA-b30079/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:49,149] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:49,149] [INFO] Task started: HMMsearch
[2023-03-16 07:28:49,149] [INFO] Running command: hmmsearch --tblout OceanDNA-b30079/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference/reference_markers.hmm OceanDNA-b30079/protein.faa > /dev/null
[2023-03-16 07:28:49,336] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:49,337] [INFO] Found 6/6 markers.
[2023-03-16 07:28:49,360] [INFO] Query marker FASTA was written to OceanDNA-b30079/markers.fasta
[2023-03-16 07:28:49,361] [INFO] Task started: Blastn
[2023-03-16 07:28:49,361] [INFO] Running command: blastn -query OceanDNA-b30079/markers.fasta -db /var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference/reference_markers.fasta -out OceanDNA-b30079/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:50,211] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:50,212] [INFO] Selected 28 target genomes.
[2023-03-16 07:28:50,213] [INFO] Target genome list was writen to OceanDNA-b30079/target_genomes.txt
[2023-03-16 07:28:50,231] [INFO] Task started: fastANI
[2023-03-16 07:28:50,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e7fb3b-26a1-4fce-beb2-e739a94dda17/OceanDNA-b30079.fa --refList OceanDNA-b30079/target_genomes.txt --output OceanDNA-b30079/fastani_result.tsv --threads 1
[2023-03-16 07:29:10,663] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:10,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:10,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:10,678] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:10,679] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:10,679] [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	78.9701	486	946	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.925	389	946	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.8972	389	946	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.8327	420	946	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.8181	420	946	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.6893	454	946	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.6651	462	946	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.6509	462	946	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.6475	386	946	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.5862	440	946	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	78.5672	392	946	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	78.5215	403	946	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.5169	420	946	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	78.2856	360	946	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.2265	398	946	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.044	325	946	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.0126	338	946	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.8584	325	946	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.7965	345	946	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.7878	330	946	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.6141	252	946	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.4828	281	946	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.4638	286	946	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3876	240	946	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.2702	233	946	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.2454	251	946	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.2192	202	946	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.799	121	946	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:10,679] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30079/tc_result.tsv
[2023-03-16 07:29:10,679] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:10,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:10,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference/checkm_data
[2023-03-16 07:29:10,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:10,692] [INFO] Task started: CheckM
[2023-03-16 07:29:10,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30079/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30079/checkm_input OceanDNA-b30079/checkm_result
[2023-03-16 07:29:57,951] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:57,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:57,954] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:57,954] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:57,955] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30079/markers.fasta)
[2023-03-16 07:29:57,955] [INFO] Task started: Blastn
[2023-03-16 07:29:57,955] [INFO] Running command: blastn -query OceanDNA-b30079/markers.fasta -db /var/lib/cwl/stg2cab684e-40c0-49f6-995f-c1eeaee6ecc2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30079/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:59,541] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:59,542] [INFO] Selected 29 target genomes.
[2023-03-16 07:29:59,542] [INFO] Target genome list was writen to OceanDNA-b30079/target_genomes_gtdb.txt
[2023-03-16 07:29:59,963] [INFO] Task started: fastANI
[2023-03-16 07:29:59,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e7fb3b-26a1-4fce-beb2-e739a94dda17/OceanDNA-b30079.fa --refList OceanDNA-b30079/target_genomes_gtdb.txt --output OceanDNA-b30079/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:20,800] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:20,816] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:30:20,816] [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_000152625.1	s__Roseovarius nubinhibens	79.7785	542	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_009762325.1	s__Roseovarius faecimaris	78.9671	486	946	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	78.9261	387	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_009363655.1	s__Roseovarius sp009363655	78.8731	470	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_900172255.1	s__Roseovarius halotolerans	78.8473	418	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.8466	417	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003651245.1	s__Roseovarius spongiae	78.7989	469	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	78.7328	294	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCF_001441615.1	s__Roseovarius atlanticus	78.7048	463	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	78.6727	435	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.656	462	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900142765.1	s__Roseovarius litoreus	78.6372	387	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_002917925.1	s__Roseovarius confluentis	78.5958	439	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_900109455.1	s__Roseovarius azorensis	78.5676	392	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.5267	419	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	78.4558	353	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002072155.1	s__Roseovarius sp002072155	78.3834	414	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.3364	393	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.255	274	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.2313	397	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.1862	372	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.1314	304	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	78.0291	354	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.0142	339	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	77.9278	334	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	77.7965	345	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.7839	331	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.3537	287	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003254465.1	s__Fluviibacterium sp003254465	77.2715	231	946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:20,816] [INFO] GTDB search result was written to OceanDNA-b30079/result_gtdb.tsv
[2023-03-16 07:30:20,816] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:20,819] [INFO] DFAST_QC result json was written to OceanDNA-b30079/dqc_result.json
[2023-03-16 07:30:20,819] [INFO] DFAST_QC completed!
[2023-03-16 07:30:20,819] [INFO] Total running time: 0h1m51s