[2023-03-15 13:26:46,053] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:26:46,055] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:26:46,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference
[2023-03-15 13:26:47,152] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:26:47,153] [INFO] Task started: Prodigal
[2023-03-15 13:26:47,153] [INFO] Running command: cat /var/lib/cwl/stg2ff817cf-927a-4843-8f8a-dc6f65286d6f/OceanDNA-b260.fa | prodigal -d OceanDNA-b260/cds.fna -a OceanDNA-b260/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:27:10,991] [INFO] Task succeeded: Prodigal
[2023-03-15 13:27:10,992] [INFO] Task started: HMMsearch
[2023-03-15 13:27:10,992] [INFO] Running command: hmmsearch --tblout OceanDNA-b260/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference/reference_markers.hmm OceanDNA-b260/protein.faa > /dev/null
[2023-03-15 13:27:11,205] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:27:11,205] [INFO] Found 6/6 markers.
[2023-03-15 13:27:11,247] [INFO] Query marker FASTA was written to OceanDNA-b260/markers.fasta
[2023-03-15 13:27:11,249] [INFO] Task started: Blastn
[2023-03-15 13:27:11,249] [INFO] Running command: blastn -query OceanDNA-b260/markers.fasta -db /var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference/reference_markers.fasta -out OceanDNA-b260/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:27:11,979] [INFO] Task succeeded: Blastn
[2023-03-15 13:27:11,984] [INFO] Selected 31 target genomes.
[2023-03-15 13:27:11,984] [INFO] Target genome list was writen to OceanDNA-b260/target_genomes.txt
[2023-03-15 13:27:12,007] [INFO] Task started: fastANI
[2023-03-15 13:27:12,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ff817cf-927a-4843-8f8a-dc6f65286d6f/OceanDNA-b260.fa --refList OceanDNA-b260/target_genomes.txt --output OceanDNA-b260/fastani_result.tsv --threads 1
[2023-03-15 13:27:31,383] [INFO] Task succeeded: fastANI
[2023-03-15 13:27:31,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:27:31,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:27:31,390] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:27:31,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:27:31,391] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.3577	96	1284	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.8602	87	1284	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.7318	76	1284	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.7105	67	1284	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.6423	57	1284	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	74.6051	50	1284	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	74.5762	58	1284	95	below_threshold
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	74.516	53	1284	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:27:31,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b260/tc_result.tsv
[2023-03-15 13:27:31,398] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:27:31,398] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:27:31,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference/checkm_data
[2023-03-15 13:27:31,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:27:31,407] [INFO] Task started: CheckM
[2023-03-15 13:27:31,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b260/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b260/checkm_input OceanDNA-b260/checkm_result
[2023-03-15 13:28:31,418] [INFO] Task succeeded: CheckM
[2023-03-15 13:28:31,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:28:31,434] [INFO] ===== Completeness check finished =====
[2023-03-15 13:28:31,434] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:28:31,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b260/markers.fasta)
[2023-03-15 13:28:31,436] [INFO] Task started: Blastn
[2023-03-15 13:28:31,436] [INFO] Running command: blastn -query OceanDNA-b260/markers.fasta -db /var/lib/cwl/stg56c141ce-5196-4f18-ab8f-85d7aa0dd9b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b260/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:28:32,716] [INFO] Task succeeded: Blastn
[2023-03-15 13:28:32,730] [INFO] Selected 27 target genomes.
[2023-03-15 13:28:32,730] [INFO] Target genome list was writen to OceanDNA-b260/target_genomes_gtdb.txt
[2023-03-15 13:28:32,988] [INFO] Task started: fastANI
[2023-03-15 13:28:32,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ff817cf-927a-4843-8f8a-dc6f65286d6f/OceanDNA-b260.fa --refList OceanDNA-b260/target_genomes_gtdb.txt --output OceanDNA-b260/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:28:52,696] [INFO] Task succeeded: fastANI
[2023-03-15 13:28:52,708] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:28:52,708] [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_009861545.1	s__WTFV01 sp009861545	77.3591	427	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_011523845.1	s__WTFV01 sp011523845	77.28	433	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	77.1681	232	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	76.9047	261	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.7934	286	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	76.637	238	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712885.1	s__UBA8438 sp002712885	76.2372	162	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778315.1	s__UBA8438 sp005778315	76.0626	104	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.059	132	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	76.0232	130	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184105.1	s__JACPDI01 sp016184105	75.8553	99	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACPDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184455.1	s__Gp6-AA40 sp016184455	75.814	118	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	75.7291	94	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192845.1	s__Gp6-AA40 sp016192845	75.6822	117	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	75.6602	87	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	75.6168	128	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.74	99.72	0.98	0.98	4	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	75.6013	116	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_016190995.1	s__JACPPN01 sp016190995	75.5602	72	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JACPPN01;g__JACPPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	75.5282	151	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268955.1	s__WHSN01 sp018268955	75.4769	75	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	75.4701	86	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826515.1	s__CADEFD01 sp902826515	75.0708	109	1284	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:28:52,712] [INFO] GTDB search result was written to OceanDNA-b260/result_gtdb.tsv
[2023-03-15 13:28:52,716] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:28:52,721] [INFO] DFAST_QC result json was written to OceanDNA-b260/dqc_result.json
[2023-03-15 13:28:52,721] [INFO] DFAST_QC completed!
[2023-03-15 13:28:52,722] [INFO] Total running time: 0h2m7s