[2023-03-16 06:03:26,026] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:26,026] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:26,026] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference
[2023-03-16 06:03:27,133] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:27,134] [INFO] Task started: Prodigal
[2023-03-16 06:03:27,134] [INFO] Running command: cat /var/lib/cwl/stgd6d26687-5dca-4ff2-81da-defc70e14b0e/OceanDNA-b24727.fa | prodigal -d OceanDNA-b24727/cds.fna -a OceanDNA-b24727/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:44,679] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:44,679] [INFO] Task started: HMMsearch
[2023-03-16 06:03:44,679] [INFO] Running command: hmmsearch --tblout OceanDNA-b24727/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference/reference_markers.hmm OceanDNA-b24727/protein.faa > /dev/null
[2023-03-16 06:03:44,891] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:44,892] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6d26687-5dca-4ff2-81da-defc70e14b0e/OceanDNA-b24727.fa]
[2023-03-16 06:03:44,916] [INFO] Query marker FASTA was written to OceanDNA-b24727/markers.fasta
[2023-03-16 06:03:44,917] [INFO] Task started: Blastn
[2023-03-16 06:03:44,917] [INFO] Running command: blastn -query OceanDNA-b24727/markers.fasta -db /var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference/reference_markers.fasta -out OceanDNA-b24727/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:45,738] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:45,739] [INFO] Selected 26 target genomes.
[2023-03-16 06:03:45,739] [INFO] Target genome list was writen to OceanDNA-b24727/target_genomes.txt
[2023-03-16 06:03:45,757] [INFO] Task started: fastANI
[2023-03-16 06:03:45,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d26687-5dca-4ff2-81da-defc70e14b0e/OceanDNA-b24727.fa --refList OceanDNA-b24727/target_genomes.txt --output OceanDNA-b24727/fastani_result.tsv --threads 1
[2023-03-16 06:04:09,652] [INFO] Task succeeded: fastANI
[2023-03-16 06:04:09,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:04:09,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:04:09,667] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:04:09,667] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:04:09,667] [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
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	84.7103	817	1003	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.7141	226	1003	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.3564	216	1003	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.3237	230	1003	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.3121	196	1003	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.2708	269	1003	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.1928	225	1003	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.0181	162	1003	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	75.9601	213	1003	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.9598	212	1003	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.942	279	1003	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	75.9004	149	1003	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	75.8037	181	1003	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	75.7832	113	1003	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	75.7761	173	1003	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	75.7407	204	1003	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	75.7229	198	1003	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	75.7079	110	1003	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	75.6876	125	1003	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	75.6665	144	1003	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.6091	129	1003	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.6024	80	1003	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.5877	81	1003	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.548	140	1003	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.4747	148	1003	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	75.433	117	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:04:09,667] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24727/tc_result.tsv
[2023-03-16 06:04:09,667] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:04:09,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:04:09,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference/checkm_data
[2023-03-16 06:04:09,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:04:09,678] [INFO] Task started: CheckM
[2023-03-16 06:04:09,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24727/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24727/checkm_input OceanDNA-b24727/checkm_result
[2023-03-16 06:04:54,250] [INFO] Task succeeded: CheckM
[2023-03-16 06:04:54,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:04:54,279] [INFO] ===== Completeness check finished =====
[2023-03-16 06:04:54,279] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:04:54,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24727/markers.fasta)
[2023-03-16 06:04:54,281] [INFO] Task started: Blastn
[2023-03-16 06:04:54,281] [INFO] Running command: blastn -query OceanDNA-b24727/markers.fasta -db /var/lib/cwl/stgbbb4fbcd-bfea-45a0-8651-6a04e532a557/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24727/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:04:55,857] [INFO] Task succeeded: Blastn
[2023-03-16 06:04:55,858] [INFO] Selected 23 target genomes.
[2023-03-16 06:04:55,858] [INFO] Target genome list was writen to OceanDNA-b24727/target_genomes_gtdb.txt
[2023-03-16 06:04:55,900] [INFO] Task started: fastANI
[2023-03-16 06:04:55,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d26687-5dca-4ff2-81da-defc70e14b0e/OceanDNA-b24727.fa --refList OceanDNA-b24727/target_genomes_gtdb.txt --output OceanDNA-b24727/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:05:18,666] [INFO] Task succeeded: fastANI
[2023-03-16 06:05:18,679] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:05:18,679] [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_002924445.1	s__Minwuia thermotolerans	84.7178	816	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCA_016865035.1	s__Minwuia sp016865035	78.4768	484	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.7862	274	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	76.6966	228	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.5206	298	1003	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_008728835.1	s__Hypericibacter adhaerens	76.3414	193	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	76.2862	267	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.2731	271	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.2543	142	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCF_003119115.1	s__Azospirillum sp003119115	76.2231	270	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCA_009377445.1	s__WHUA01 sp009377445	76.2078	162	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	76.1849	226	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479765.1	s__Tepidamorphus sp905479765	76.0836	134	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Tepidamorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	76.0227	175	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	75.973	211	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003004785.1	s__Alsobacter soli	75.899	149	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900079695.1	s__Alpha-05 sp900079695	75.7639	150	1003	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_000751295.2	s__Phreatobacter sp000751295	75.735	224	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	75.6775	178	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	75.5923	216	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	75.5908	131	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	75.5877	81	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014654775.1	s__Gemmobacter_B sp014654775	75.2993	74	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:05:18,681] [INFO] GTDB search result was written to OceanDNA-b24727/result_gtdb.tsv
[2023-03-16 06:05:18,682] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:05:18,688] [INFO] DFAST_QC result json was written to OceanDNA-b24727/dqc_result.json
[2023-03-16 06:05:18,688] [INFO] DFAST_QC completed!
[2023-03-16 06:05:18,688] [INFO] Total running time: 0h1m53s