[2023-03-18 06:30:24,822] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,827] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference
[2023-03-18 06:30:25,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,968] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,968] [INFO] Running command: cat /var/lib/cwl/stg67b86c1a-dd6f-42a9-8a20-22f8449b3c4d/OceanDNA-b30168.fa | prodigal -d OceanDNA-b30168/cds.fna -a OceanDNA-b30168/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:38,945] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:38,945] [INFO] Task started: HMMsearch
[2023-03-18 06:30:38,945] [INFO] Running command: hmmsearch --tblout OceanDNA-b30168/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference/reference_markers.hmm OceanDNA-b30168/protein.faa > /dev/null
[2023-03-18 06:30:39,099] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:39,100] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg67b86c1a-dd6f-42a9-8a20-22f8449b3c4d/OceanDNA-b30168.fa]
[2023-03-18 06:30:39,122] [INFO] Query marker FASTA was written to OceanDNA-b30168/markers.fasta
[2023-03-18 06:30:39,122] [INFO] Task started: Blastn
[2023-03-18 06:30:39,122] [INFO] Running command: blastn -query OceanDNA-b30168/markers.fasta -db /var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference/reference_markers.fasta -out OceanDNA-b30168/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:39,562] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:39,565] [INFO] Selected 17 target genomes.
[2023-03-18 06:30:39,566] [INFO] Target genome list was writen to OceanDNA-b30168/target_genomes.txt
[2023-03-18 06:30:39,637] [INFO] Task started: fastANI
[2023-03-18 06:30:39,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b86c1a-dd6f-42a9-8a20-22f8449b3c4d/OceanDNA-b30168.fa --refList OceanDNA-b30168/target_genomes.txt --output OceanDNA-b30168/fastani_result.tsv --threads 1
[2023-03-18 06:30:50,488] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:50,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:50,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:50,496] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:50,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:30:50,496] [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
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	78.7057	306	626	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	77.9019	256	626	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.8863	239	626	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.8823	236	626	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.0741	139	626	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.9298	126	626	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.921	118	626	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.8057	113	626	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	76.702	116	626	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	76.198	63	626	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	76.198	63	626	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:30:50,502] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30168/tc_result.tsv
[2023-03-18 06:30:50,510] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:50,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:50,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference/checkm_data
[2023-03-18 06:30:50,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:50,545] [INFO] Task started: CheckM
[2023-03-18 06:30:50,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30168/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30168/checkm_input OceanDNA-b30168/checkm_result
[2023-03-18 06:31:26,830] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:26,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.81%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:26,889] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:26,889] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:26,889] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30168/markers.fasta)
[2023-03-18 06:31:26,890] [INFO] Task started: Blastn
[2023-03-18 06:31:26,890] [INFO] Running command: blastn -query OceanDNA-b30168/markers.fasta -db /var/lib/cwl/stg2241a98e-36b2-40c7-8173-d33b607f9e5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30168/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:27,370] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:27,390] [INFO] Selected 15 target genomes.
[2023-03-18 06:31:27,390] [INFO] Target genome list was writen to OceanDNA-b30168/target_genomes_gtdb.txt
[2023-03-18 06:31:27,440] [INFO] Task started: fastANI
[2023-03-18 06:31:27,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b86c1a-dd6f-42a9-8a20-22f8449b3c4d/OceanDNA-b30168.fa --refList OceanDNA-b30168/target_genomes_gtdb.txt --output OceanDNA-b30168/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:37,811] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:37,820] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:31:37,820] [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_003610455.1	s__Sulfitobacter guttiformis	78.7263	304	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196805.1	s__Sulfitobacter undariae	77.9071	255	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	77.8917	238	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.4952	194	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.2789	132	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106935.1	s__Sulfitobacter pontiacus	76.9298	126	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_900112755.1	s__Sulfitobacter brevis	76.9219	121	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	76.8076	112	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_900113435.1	s__Sulfitobacter dubius	76.703	115	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_003352065.1	s__Sulfitobacter sp003352065	76.6328	123	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352085.1	s__Sulfitobacter sp003352085	76.599	137	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001681715.1	s__Epibacterium mobile	76.2204	61	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_001886735.1	s__Sulfitobacter alexandrii	76.0492	96	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	75.9769	58	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_013033515.1	s__Ruegeria sp013033515	75.8257	53	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:37,828] [INFO] GTDB search result was written to OceanDNA-b30168/result_gtdb.tsv
[2023-03-18 06:31:37,839] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:37,849] [INFO] DFAST_QC result json was written to OceanDNA-b30168/dqc_result.json
[2023-03-18 06:31:37,850] [INFO] DFAST_QC completed!
[2023-03-18 06:31:37,850] [INFO] Total running time: 0h1m13s