[2023-03-18 00:35:04,579] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,580] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference
[2023-03-18 00:35:05,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,644] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,644] [INFO] Running command: cat /var/lib/cwl/stg4c669f79-03ae-4910-8227-865905a6f20e/OceanDNA-b32764.fa | prodigal -d OceanDNA-b32764/cds.fna -a OceanDNA-b32764/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:27,938] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:27,938] [INFO] Task started: HMMsearch
[2023-03-18 00:35:27,938] [INFO] Running command: hmmsearch --tblout OceanDNA-b32764/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference/reference_markers.hmm OceanDNA-b32764/protein.faa > /dev/null
[2023-03-18 00:35:28,195] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:28,196] [INFO] Found 6/6 markers.
[2023-03-18 00:35:28,217] [INFO] Query marker FASTA was written to OceanDNA-b32764/markers.fasta
[2023-03-18 00:35:28,217] [INFO] Task started: Blastn
[2023-03-18 00:35:28,217] [INFO] Running command: blastn -query OceanDNA-b32764/markers.fasta -db /var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference/reference_markers.fasta -out OceanDNA-b32764/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:28,980] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:28,980] [INFO] Selected 35 target genomes.
[2023-03-18 00:35:28,981] [INFO] Target genome list was writen to OceanDNA-b32764/target_genomes.txt
[2023-03-18 00:35:28,993] [INFO] Task started: fastANI
[2023-03-18 00:35:28,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c669f79-03ae-4910-8227-865905a6f20e/OceanDNA-b32764.fa --refList OceanDNA-b32764/target_genomes.txt --output OceanDNA-b32764/fastani_result.tsv --threads 1
[2023-03-18 00:35:58,178] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:58,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:58,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:58,195] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:58,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:35:58,195] [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
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.3053	134	1168	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.242	102	1168	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.2381	118	1168	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.2168	127	1168	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.1886	152	1168	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.1819	158	1168	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.1497	156	1168	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.1448	155	1168	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	76.1171	70	1168	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.1065	114	1168	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.0716	177	1168	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.0688	180	1168	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0632	153	1168	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.047	132	1168	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.0416	125	1168	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.0245	101	1168	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.0149	114	1168	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.0144	89	1168	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.9167	108	1168	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.88	81	1168	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8283	136	1168	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	75.8258	93	1168	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.8128	69	1168	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	75.7514	67	1168	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.7165	92	1168	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.696	104	1168	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	75.6882	79	1168	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.6447	65	1168	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	75.6155	62	1168	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.5064	82	1168	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	75.4552	88	1168	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.286	93	1168	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:35:58,195] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32764/tc_result.tsv
[2023-03-18 00:35:58,195] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:58,195] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:58,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference/checkm_data
[2023-03-18 00:35:58,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:58,201] [INFO] Task started: CheckM
[2023-03-18 00:35:58,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32764/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32764/checkm_input OceanDNA-b32764/checkm_result
[2023-03-18 00:36:53,840] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:53,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:53,843] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:53,843] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:53,843] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32764/markers.fasta)
[2023-03-18 00:36:53,844] [INFO] Task started: Blastn
[2023-03-18 00:36:53,844] [INFO] Running command: blastn -query OceanDNA-b32764/markers.fasta -db /var/lib/cwl/stg5c6ead81-c616-4cb6-89a8-7d53384083c7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32764/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:55,274] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:55,275] [INFO] Selected 12 target genomes.
[2023-03-18 00:36:55,275] [INFO] Target genome list was writen to OceanDNA-b32764/target_genomes_gtdb.txt
[2023-03-18 00:36:55,285] [INFO] Task started: fastANI
[2023-03-18 00:36:55,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c669f79-03ae-4910-8227-865905a6f20e/OceanDNA-b32764.fa --refList OceanDNA-b32764/target_genomes_gtdb.txt --output OceanDNA-b32764/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:37:03,230] [INFO] Task succeeded: fastANI
[2023-03-18 00:37:03,237] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:37:03,237] [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_018667335.1	s__UBA8079 sp018667335	88.8802	938	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_018702955.1	s__UBA8079 sp018702955	84.7711	826	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002727315.1	s__UBA8079 sp002727315	79.7916	448	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	79.321	492	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.6125	389	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	77.9213	259	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	77.5617	289	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.3069	130	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	75.7312	68	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763885.1	s__Paracoccus versutus	75.6245	88	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_014645695.1	s__Salinarimonas ramus	75.4599	90	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:37:03,237] [INFO] GTDB search result was written to OceanDNA-b32764/result_gtdb.tsv
[2023-03-18 00:37:03,237] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:37:03,239] [INFO] DFAST_QC result json was written to OceanDNA-b32764/dqc_result.json
[2023-03-18 00:37:03,240] [INFO] DFAST_QC completed!
[2023-03-18 00:37:03,240] [INFO] Total running time: 0h1m59s