[2023-03-15 21:32:41,289] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:32:41,289] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:32:41,289] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference
[2023-03-15 21:32:42,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:32:42,946] [INFO] Task started: Prodigal
[2023-03-15 21:32:42,946] [INFO] Running command: cat /var/lib/cwl/stgf5d301e1-f4f7-42aa-8e23-14a8ab1a33ae/OceanDNA-b31425.fa | prodigal -d OceanDNA-b31425/cds.fna -a OceanDNA-b31425/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:33:05,362] [INFO] Task succeeded: Prodigal
[2023-03-15 21:33:05,362] [INFO] Task started: HMMsearch
[2023-03-15 21:33:05,362] [INFO] Running command: hmmsearch --tblout OceanDNA-b31425/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference/reference_markers.hmm OceanDNA-b31425/protein.faa > /dev/null
[2023-03-15 21:33:05,578] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:33:05,578] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf5d301e1-f4f7-42aa-8e23-14a8ab1a33ae/OceanDNA-b31425.fa]
[2023-03-15 21:33:05,605] [INFO] Query marker FASTA was written to OceanDNA-b31425/markers.fasta
[2023-03-15 21:33:05,606] [INFO] Task started: Blastn
[2023-03-15 21:33:05,606] [INFO] Running command: blastn -query OceanDNA-b31425/markers.fasta -db /var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference/reference_markers.fasta -out OceanDNA-b31425/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:33:06,241] [INFO] Task succeeded: Blastn
[2023-03-15 21:33:06,242] [INFO] Selected 35 target genomes.
[2023-03-15 21:33:06,242] [INFO] Target genome list was writen to OceanDNA-b31425/target_genomes.txt
[2023-03-15 21:33:06,308] [INFO] Task started: fastANI
[2023-03-15 21:33:06,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d301e1-f4f7-42aa-8e23-14a8ab1a33ae/OceanDNA-b31425.fa --refList OceanDNA-b31425/target_genomes.txt --output OceanDNA-b31425/fastani_result.tsv --threads 1
[2023-03-15 21:33:35,728] [INFO] Task succeeded: fastANI
[2023-03-15 21:33:35,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:33:35,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:33:35,746] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:33:35,746] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:33:35,746] [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
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.7963	297	1182	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.7428	298	1182	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.742	239	1182	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.5962	241	1182	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.5742	200	1182	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.5491	178	1182	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.5305	202	1182	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.4112	138	1182	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.3924	208	1182	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.3817	167	1182	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.3715	239	1182	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.3482	163	1182	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.3073	116	1182	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3053	234	1182	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.2779	129	1182	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2764	158	1182	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	76.1163	126	1182	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.0913	129	1182	95	below_threshold
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	76.0641	89	1182	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.041	156	1182	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	76.0161	178	1182	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	75.9559	66	1182	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.9391	145	1182	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	75.91	136	1182	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.8822	190	1182	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.8737	130	1182	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	75.8538	159	1182	95	below_threshold
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	75.8379	120	1182	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.8329	94	1182	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	75.8239	62	1182	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	75.7869	62	1182	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.6588	108	1182	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	75.6553	162	1182	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	75.338	50	1182	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:33:35,749] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31425/tc_result.tsv
[2023-03-15 21:33:35,753] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:33:35,753] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:33:35,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference/checkm_data
[2023-03-15 21:33:35,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:33:35,762] [INFO] Task started: CheckM
[2023-03-15 21:33:35,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31425/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31425/checkm_input OceanDNA-b31425/checkm_result
[2023-03-15 21:34:32,834] [INFO] Task succeeded: CheckM
[2023-03-15 21:34:32,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:34:32,967] [INFO] ===== Completeness check finished =====
[2023-03-15 21:34:32,967] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:34:32,968] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31425/markers.fasta)
[2023-03-15 21:34:32,969] [INFO] Task started: Blastn
[2023-03-15 21:34:32,969] [INFO] Running command: blastn -query OceanDNA-b31425/markers.fasta -db /var/lib/cwl/stgbf1a6adc-c722-4988-a221-b434832fd10a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31425/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:34:33,992] [INFO] Task succeeded: Blastn
[2023-03-15 21:34:33,993] [INFO] Selected 32 target genomes.
[2023-03-15 21:34:33,993] [INFO] Target genome list was writen to OceanDNA-b31425/target_genomes_gtdb.txt
[2023-03-15 21:34:35,345] [INFO] Task started: fastANI
[2023-03-15 21:34:35,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d301e1-f4f7-42aa-8e23-14a8ab1a33ae/OceanDNA-b31425.fa --refList OceanDNA-b31425/target_genomes_gtdb.txt --output OceanDNA-b31425/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:35:01,479] [INFO] Task succeeded: fastANI
[2023-03-15 21:35:01,496] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:35:01,496] [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_014323865.1	s__SP197 sp014323865	78.3703	350	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722885.1	s__SP197 sp002722885	78.163	415	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700655.1	s__SP197 sp018700655	77.9369	402	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	99.23	99.15	0.84	0.82	5	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.8054	185	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_900177295.1	s__Tistlia consotensis	76.8043	296	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014925385.1	s__WHTV01 sp014925385	76.7333	241	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.7225	120	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_013003675.1	s__JABDIP01 sp013003675	76.6427	119	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869515.1	s__VGDZ01 sp016869515	76.6244	159	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VGDZ01;f__VGDZ01;g__VGDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.614	242	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	76.5502	149	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.5499	74	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792565.1	s__UBA2784 sp016792565	76.4821	139	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__UBA2784	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	76.435	216	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	76.4254	162	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.4058	110	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	76.4043	218	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	76.376	215	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	76.3727	236	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.332	172	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016185145.1	s__Reyranella sp016185145	76.3178	195	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	76.2699	228	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013340935.1	s__Azospirillum melinis	76.1988	225	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_003116035.1	s__Azospirillum sp003116035	76.1527	218	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690215.1	s__GCA-2690215 sp002690215	76.0986	114	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780605.1	s__Reyranella sp016780605	76.0969	127	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	76.0804	130	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016107285.1	s__Roseomonas sp016107285	76.04	163	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	75.8239	62	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455965.1	s__Methylobacterium sp001455965	75.7741	127	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:35:01,505] [INFO] GTDB search result was written to OceanDNA-b31425/result_gtdb.tsv
[2023-03-15 21:35:01,524] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:35:01,535] [INFO] DFAST_QC result json was written to OceanDNA-b31425/dqc_result.json
[2023-03-15 21:35:01,535] [INFO] DFAST_QC completed!
[2023-03-15 21:35:01,535] [INFO] Total running time: 0h2m20s