[2023-03-18 01:26:26,283] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference
[2023-03-18 01:26:27,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,426] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,427] [INFO] Running command: cat /var/lib/cwl/stg6473e456-8aaa-46cb-8edc-b2cb0b61247b/OceanDNA-b156.fa | prodigal -d OceanDNA-b156/cds.fna -a OceanDNA-b156/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:47,140] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:47,140] [INFO] Task started: HMMsearch
[2023-03-18 01:26:47,140] [INFO] Running command: hmmsearch --tblout OceanDNA-b156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference/reference_markers.hmm OceanDNA-b156/protein.faa > /dev/null
[2023-03-18 01:26:47,403] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:47,404] [INFO] Found 6/6 markers.
[2023-03-18 01:26:47,424] [INFO] Query marker FASTA was written to OceanDNA-b156/markers.fasta
[2023-03-18 01:26:47,425] [INFO] Task started: Blastn
[2023-03-18 01:26:47,426] [INFO] Running command: blastn -query OceanDNA-b156/markers.fasta -db /var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference/reference_markers.fasta -out OceanDNA-b156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:48,027] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:48,028] [INFO] Selected 29 target genomes.
[2023-03-18 01:26:48,028] [INFO] Target genome list was writen to OceanDNA-b156/target_genomes.txt
[2023-03-18 01:26:48,104] [INFO] Task started: fastANI
[2023-03-18 01:26:48,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg6473e456-8aaa-46cb-8edc-b2cb0b61247b/OceanDNA-b156.fa --refList OceanDNA-b156/target_genomes.txt --output OceanDNA-b156/fastani_result.tsv --threads 1
[2023-03-18 01:27:09,539] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:09,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:27:09,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:27:09,548] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:27:09,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:27:09,548] [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	76.2346	148	1081	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	74.8707	86	1081	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	74.8706	93	1081	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.8643	79	1081	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.8275	81	1081	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.7898	88	1081	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	74.7801	60	1081	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.7684	106	1081	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.727	92	1081	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	74.6977	57	1081	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.6868	69	1081	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	74.616	56	1081	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:27:09,548] [INFO] DFAST Taxonomy check result was written to OceanDNA-b156/tc_result.tsv
[2023-03-18 01:27:09,549] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:27:09,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:27:09,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference/checkm_data
[2023-03-18 01:27:09,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:27:09,554] [INFO] Task started: CheckM
[2023-03-18 01:27:09,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b156/checkm_input OceanDNA-b156/checkm_result
[2023-03-18 01:27:58,738] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:58,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:58,741] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:58,741] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:58,741] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b156/markers.fasta)
[2023-03-18 01:27:58,741] [INFO] Task started: Blastn
[2023-03-18 01:27:58,741] [INFO] Running command: blastn -query OceanDNA-b156/markers.fasta -db /var/lib/cwl/stg10194909-9275-4eab-83f7-57d9de21b418/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:59,617] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:59,617] [INFO] Selected 19 target genomes.
[2023-03-18 01:27:59,617] [INFO] Target genome list was writen to OceanDNA-b156/target_genomes_gtdb.txt
[2023-03-18 01:27:59,676] [INFO] Task started: fastANI
[2023-03-18 01:27:59,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg6473e456-8aaa-46cb-8edc-b2cb0b61247b/OceanDNA-b156.fa --refList OceanDNA-b156/target_genomes_gtdb.txt --output OceanDNA-b156/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:28:13,626] [INFO] Task succeeded: fastANI
[2023-03-18 01:28:13,636] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:28:13,637] [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_002730525.1	s__UBA2161 sp002730525	99.9829	1050	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002328835.1	s__UBA2161 sp002328835	90.415	993	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_002296225.1	s__UBA823 sp002296225	77.1321	205	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA823	95.0	99.57	99.38	0.83	0.81	4	-
GCA_016195265.1	s__Gp6-AA45 sp016195265	76.5846	158	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	76.4025	136	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
GCA_001767525.1	s__Gp6-AA40 sp001767525	76.3455	142	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.96	99.96	0.95	0.95	2	-
GCA_002730735.1	s__UBA11600 sp002730735	76.3347	56	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	76.3127	171	1081	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_011523845.1	s__WTFV01 sp011523845	76.272	221	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	76.2555	197	1081	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_016650245.1	s__JAENWD01 sp016650245	76.2526	117	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JAENWD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717745.1	s__UBA11600 sp002717745	76.2475	58	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860085.1	s__JAFNAJ01 sp017860085	76.1892	111	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JAFNAJ01;g__JAFNAJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223835.1	s__Gp6-AA38 sp003223835	76.1261	168	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__Gp6-AA38	95.0	98.48	98.48	0.89	0.89	2	-
GCA_003223775.1	s__Gp6-AA45 sp003223775	76.1164	157	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	76.0611	171	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_016178075.1	s__JACQTH01 sp016178075	75.9965	119	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JACQTH01;g__JACQTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865485.1	s__Luteitalea sp016865485	75.9735	191	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195295.1	s__Gp6-AA45 sp016195295	75.8776	111	1081	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:28:13,637] [INFO] GTDB search result was written to OceanDNA-b156/result_gtdb.tsv
[2023-03-18 01:28:13,637] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:28:13,638] [INFO] DFAST_QC result json was written to OceanDNA-b156/dqc_result.json
[2023-03-18 01:28:13,639] [INFO] DFAST_QC completed!
[2023-03-18 01:28:13,639] [INFO] Total running time: 0h1m47s