[2023-03-18 10:12:10,248] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,248] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference
[2023-03-18 10:12:11,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,378] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,378] [INFO] Running command: cat /var/lib/cwl/stgcf1098c1-f97a-45c7-a612-2bc65aed0c82/OceanDNA-b262.fa | prodigal -d OceanDNA-b262/cds.fna -a OceanDNA-b262/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:37,248] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:37,248] [INFO] Task started: HMMsearch
[2023-03-18 10:12:37,248] [INFO] Running command: hmmsearch --tblout OceanDNA-b262/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference/reference_markers.hmm OceanDNA-b262/protein.faa > /dev/null
[2023-03-18 10:12:37,457] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:37,457] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcf1098c1-f97a-45c7-a612-2bc65aed0c82/OceanDNA-b262.fa]
[2023-03-18 10:12:37,486] [INFO] Query marker FASTA was written to OceanDNA-b262/markers.fasta
[2023-03-18 10:12:37,487] [INFO] Task started: Blastn
[2023-03-18 10:12:37,487] [INFO] Running command: blastn -query OceanDNA-b262/markers.fasta -db /var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference/reference_markers.fasta -out OceanDNA-b262/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:38,162] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:38,163] [INFO] Selected 29 target genomes.
[2023-03-18 10:12:38,164] [INFO] Target genome list was writen to OceanDNA-b262/target_genomes.txt
[2023-03-18 10:12:38,180] [INFO] Task started: fastANI
[2023-03-18 10:12:38,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf1098c1-f97a-45c7-a612-2bc65aed0c82/OceanDNA-b262.fa --refList OceanDNA-b262/target_genomes.txt --output OceanDNA-b262/fastani_result.tsv --threads 1
[2023-03-18 10:13:04,546] [INFO] Task succeeded: fastANI
[2023-03-18 10:13:04,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:13:04,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:13:04,558] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:13:04,558] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:13:04,558] [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	75.4944	129	1384	95	below_threshold
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	74.8023	87	1384	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.7915	85	1384	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	74.7899	86	1384	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.7614	100	1384	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	74.7453	70	1384	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.7415	73	1384	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	74.7268	57	1384	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.7228	72	1384	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	74.7202	58	1384	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	74.7202	58	1384	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	74.7167	88	1384	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.7132	62	1384	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.6987	64	1384	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	74.6746	107	1384	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.6679	114	1384	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	74.6195	104	1384	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	74.5725	79	1384	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:13:04,558] [INFO] DFAST Taxonomy check result was written to OceanDNA-b262/tc_result.tsv
[2023-03-18 10:13:04,558] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:13:04,558] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:13:04,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference/checkm_data
[2023-03-18 10:13:04,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:13:04,565] [INFO] Task started: CheckM
[2023-03-18 10:13:04,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b262/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b262/checkm_input OceanDNA-b262/checkm_result
[2023-03-18 10:14:08,939] [INFO] Task succeeded: CheckM
[2023-03-18 10:14:08,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:14:08,942] [INFO] ===== Completeness check finished =====
[2023-03-18 10:14:08,943] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:14:08,943] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b262/markers.fasta)
[2023-03-18 10:14:08,944] [INFO] Task started: Blastn
[2023-03-18 10:14:08,944] [INFO] Running command: blastn -query OceanDNA-b262/markers.fasta -db /var/lib/cwl/stgaaa7b5ad-7c37-4403-9280-3d1513f0c87c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b262/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:14:10,927] [INFO] Task succeeded: Blastn
[2023-03-18 10:14:10,928] [INFO] Selected 19 target genomes.
[2023-03-18 10:14:10,928] [INFO] Target genome list was writen to OceanDNA-b262/target_genomes_gtdb.txt
[2023-03-18 10:14:10,956] [INFO] Task started: fastANI
[2023-03-18 10:14:10,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf1098c1-f97a-45c7-a612-2bc65aed0c82/OceanDNA-b262.fa --refList OceanDNA-b262/target_genomes_gtdb.txt --output OceanDNA-b262/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:14:26,228] [INFO] Task succeeded: fastANI
[2023-03-18 10:14:26,239] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:14:26,240] [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	77.5192	483	1384	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	77.4495	502	1384	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	77.0452	252	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.8964	323	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	76.8944	287	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838525.1	s__VXRJ01 sp009838525	76.8923	333	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__VXRJ01	95.0	98.98	98.07	0.95	0.93	4	-
GCA_002726085.1	s__NP936 sp002726085	76.6968	286	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.0834	170	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_002730525.1	s__UBA2161 sp002730525	76.0534	146	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	75.9864	154	1384	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_003242705.1	s__SCN-69-37 sp003242705	75.9643	111	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SCN-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	75.959	135	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694635.1	s__JACDCA01 sp013694635	75.9584	66	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860085.1	s__JAFNAJ01 sp017860085	75.9266	82	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JAFNAJ01;g__JAFNAJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184105.1	s__JACPDI01 sp016184105	75.8244	132	1384	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_017883185.1	s__FEN-299 sp017883185	75.7755	98	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__FEN-299	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380045.1	s__WHSN01 sp009380045	75.6833	102	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	75.5164	182	1384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	75.4848	128	1384	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	-
--------------------------------------------------------------------------------
[2023-03-18 10:14:26,240] [INFO] GTDB search result was written to OceanDNA-b262/result_gtdb.tsv
[2023-03-18 10:14:26,240] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:14:26,242] [INFO] DFAST_QC result json was written to OceanDNA-b262/dqc_result.json
[2023-03-18 10:14:26,242] [INFO] DFAST_QC completed!
[2023-03-18 10:14:26,242] [INFO] Total running time: 0h2m16s