[2023-03-18 08:55:50,608] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,609] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference
[2023-03-18 08:55:51,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,781] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,782] [INFO] Running command: cat /var/lib/cwl/stg7eeb8a89-4a27-442a-87b1-32fd89ccbe66/OceanDNA-b23312.fa | prodigal -d OceanDNA-b23312/cds.fna -a OceanDNA-b23312/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:11,356] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:11,356] [INFO] Task started: HMMsearch
[2023-03-18 08:56:11,356] [INFO] Running command: hmmsearch --tblout OceanDNA-b23312/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference/reference_markers.hmm OceanDNA-b23312/protein.faa > /dev/null
[2023-03-18 08:56:11,624] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:11,625] [INFO] Found 6/6 markers.
[2023-03-18 08:56:11,656] [INFO] Query marker FASTA was written to OceanDNA-b23312/markers.fasta
[2023-03-18 08:56:11,657] [INFO] Task started: Blastn
[2023-03-18 08:56:11,658] [INFO] Running command: blastn -query OceanDNA-b23312/markers.fasta -db /var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference/reference_markers.fasta -out OceanDNA-b23312/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:12,461] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:12,462] [INFO] Selected 41 target genomes.
[2023-03-18 08:56:12,463] [INFO] Target genome list was writen to OceanDNA-b23312/target_genomes.txt
[2023-03-18 08:56:12,493] [INFO] Task started: fastANI
[2023-03-18 08:56:12,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eeb8a89-4a27-442a-87b1-32fd89ccbe66/OceanDNA-b23312.fa --refList OceanDNA-b23312/target_genomes.txt --output OceanDNA-b23312/fastani_result.tsv --threads 1
[2023-03-18 08:56:43,441] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:43,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:43,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:43,457] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:43,457] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:43,457] [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
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1942	107	1045	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1526	113	1045	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0839	85	1045	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0838	93	1045	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.036	75	1045	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.0149	81	1045	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.0027	94	1045	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.972	87	1045	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.9564	85	1045	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	75.9354	55	1045	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.9018	94	1045	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.8114	130	1045	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	75.7919	61	1045	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.7637	110	1045	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.6579	118	1045	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.6485	119	1045	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.643	69	1045	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.6207	56	1045	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.5963	65	1045	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.5731	66	1045	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	75.5657	72	1045	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	75.5248	71	1045	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.4955	86	1045	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	75.4389	59	1045	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	75.3969	57	1045	95	below_threshold
Elstera cyanobacteriorum	strain=CGMCC 1.15802	GCA_014643715.1	2022747	2022747	type	True	75.3855	50	1045	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	75.3289	86	1045	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	75.3283	60	1045	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:43,457] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23312/tc_result.tsv
[2023-03-18 08:56:43,457] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:43,457] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:43,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference/checkm_data
[2023-03-18 08:56:43,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:43,466] [INFO] Task started: CheckM
[2023-03-18 08:56:43,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23312/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23312/checkm_input OceanDNA-b23312/checkm_result
[2023-03-18 08:57:32,822] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:32,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:33,137] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:33,137] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:33,137] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23312/markers.fasta)
[2023-03-18 08:57:33,138] [INFO] Task started: Blastn
[2023-03-18 08:57:33,138] [INFO] Running command: blastn -query OceanDNA-b23312/markers.fasta -db /var/lib/cwl/stgc3099d27-0539-48fe-b5d6-7b0114250b85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23312/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:34,268] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:34,269] [INFO] Selected 43 target genomes.
[2023-03-18 08:57:34,269] [INFO] Target genome list was writen to OceanDNA-b23312/target_genomes_gtdb.txt
[2023-03-18 08:57:34,298] [INFO] Task started: fastANI
[2023-03-18 08:57:34,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eeb8a89-4a27-442a-87b1-32fd89ccbe66/OceanDNA-b23312.fa --refList OceanDNA-b23312/target_genomes_gtdb.txt --output OceanDNA-b23312/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:58:03,109] [INFO] Task succeeded: fastANI
[2023-03-18 08:58:03,124] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:58:03,124] [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_003336875.1	s__Oleisolibacter albus	76.4034	71	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.3248	89	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.1665	112	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	76.1034	60	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.1017	92	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.0839	85	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.019	93	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCF_017355985.1	s__Desertibacter sp017355985	76.0149	81	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870115.1	s__VGCH01 sp016870115	76.0094	63	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__VGCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238885.1	s__Bin95 sp002238885	76.0086	64	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin95;f__Bin95;g__Bin95	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315795.1	s__Caenispirillum salinarum	75.972	87	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	75.9564	85	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356015.1	s__Azospirillum sp017356015	75.9347	98	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	75.9018	94	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840595.1	s__Bin65 sp009840595	75.795	79	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	98.91	96.90	0.94	0.92	4	-
GCF_002073975.1	s__Rhodovulum sp002073975	75.7545	52	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	75.7529	111	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009909005.1	s__JAAAOG01 sp009909005	75.7013	67	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JAAAOG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937115.1	s__Rhodopila globiformis	75.6967	101	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	75.6934	109	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	75.6751	70	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	75.6634	111	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.6579	118	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017643325.1	s__JABJAG01 sp017643325	75.6367	57	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	75.6219	68	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	75.6207	56	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	75.6148	62	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848505.1	s__Roseomonas deserti_A	75.3969	57	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	75.1322	54	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:58:03,125] [INFO] GTDB search result was written to OceanDNA-b23312/result_gtdb.tsv
[2023-03-18 08:58:03,125] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:58:03,128] [INFO] DFAST_QC result json was written to OceanDNA-b23312/dqc_result.json
[2023-03-18 08:58:03,128] [INFO] DFAST_QC completed!
[2023-03-18 08:58:03,128] [INFO] Total running time: 0h2m13s