[2023-03-17 05:26:45,786] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,788] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference
[2023-03-17 05:26:46,921] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,921] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,921] [INFO] Running command: cat /var/lib/cwl/stg4672f0de-16e3-4522-8d32-ae398580342f/OceanDNA-b31429.fa | prodigal -d OceanDNA-b31429/cds.fna -a OceanDNA-b31429/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:27:09,545] [INFO] Task succeeded: Prodigal
[2023-03-17 05:27:09,545] [INFO] Task started: HMMsearch
[2023-03-17 05:27:09,545] [INFO] Running command: hmmsearch --tblout OceanDNA-b31429/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference/reference_markers.hmm OceanDNA-b31429/protein.faa > /dev/null
[2023-03-17 05:27:09,740] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:27:09,740] [INFO] Found 6/6 markers.
[2023-03-17 05:27:09,763] [INFO] Query marker FASTA was written to OceanDNA-b31429/markers.fasta
[2023-03-17 05:27:09,763] [INFO] Task started: Blastn
[2023-03-17 05:27:09,763] [INFO] Running command: blastn -query OceanDNA-b31429/markers.fasta -db /var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference/reference_markers.fasta -out OceanDNA-b31429/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:10,540] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:10,541] [INFO] Selected 31 target genomes.
[2023-03-17 05:27:10,542] [INFO] Target genome list was writen to OceanDNA-b31429/target_genomes.txt
[2023-03-17 05:27:10,557] [INFO] Task started: fastANI
[2023-03-17 05:27:10,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg4672f0de-16e3-4522-8d32-ae398580342f/OceanDNA-b31429.fa --refList OceanDNA-b31429/target_genomes.txt --output OceanDNA-b31429/fastani_result.tsv --threads 1
[2023-03-17 05:27:32,838] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:32,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:32,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:32,854] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:27:32,854] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:27:32,854] [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
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.4121	104	1183	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4089	104	1183	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.4001	89	1183	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3189	118	1183	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2759	89	1183	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.2141	98	1183	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.1884	79	1183	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.1841	85	1183	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.1711	81	1183	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.1539	81	1183	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.0793	134	1183	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.0192	108	1183	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.0027	118	1183	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.9961	115	1183	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.994	115	1183	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.9249	64	1183	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	75.9242	88	1183	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	75.9202	55	1183	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	75.8636	62	1183	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	75.8154	77	1183	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.7735	139	1183	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	75.7487	52	1183	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	75.7242	51	1183	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	75.6306	70	1183	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.6203	60	1183	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	75.6018	99	1183	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.5874	53	1183	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	75.474	58	1183	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.3811	62	1183	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:27:32,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31429/tc_result.tsv
[2023-03-17 05:27:32,855] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:32,855] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:32,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference/checkm_data
[2023-03-17 05:27:32,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:32,861] [INFO] Task started: CheckM
[2023-03-17 05:27:32,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31429/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31429/checkm_input OceanDNA-b31429/checkm_result
[2023-03-17 05:28:30,047] [INFO] Task succeeded: CheckM
[2023-03-17 05:28:30,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:28:30,302] [INFO] ===== Completeness check finished =====
[2023-03-17 05:28:30,303] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:28:30,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31429/markers.fasta)
[2023-03-17 05:28:30,304] [INFO] Task started: Blastn
[2023-03-17 05:28:30,304] [INFO] Running command: blastn -query OceanDNA-b31429/markers.fasta -db /var/lib/cwl/stg7f511443-1547-43f6-96f7-94f4f8e084d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31429/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:28:31,834] [INFO] Task succeeded: Blastn
[2023-03-17 05:28:31,835] [INFO] Selected 23 target genomes.
[2023-03-17 05:28:31,835] [INFO] Target genome list was writen to OceanDNA-b31429/target_genomes_gtdb.txt
[2023-03-17 05:28:32,194] [INFO] Task started: fastANI
[2023-03-17 05:28:32,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg4672f0de-16e3-4522-8d32-ae398580342f/OceanDNA-b31429.fa --refList OceanDNA-b31429/target_genomes_gtdb.txt --output OceanDNA-b31429/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:28:49,257] [INFO] Task succeeded: fastANI
[2023-03-17 05:28:49,269] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:28:49,269] [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_002722885.1	s__SP197 sp002722885	99.9119	1176	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018700655.1	s__SP197 sp018700655	78.9951	523	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	99.23	99.15	0.84	0.82	5	-
GCA_014323865.1	s__SP197 sp014323865	78.7428	437	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.5715	84	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238685.1	s__MPMV01 sp002238685	76.5396	162	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__MPMV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.3792	79	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.3575	99	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.2628	104	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	76.2559	54	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_017963645.1	s__Marivibrio halodurans	76.1884	79	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.1626	106	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.0432	132	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	76.043	80	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	75.9396	87	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_016780605.1	s__Reyranella sp016780605	75.8199	74	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	75.8149	116	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	75.7875	89	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.7793	115	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.6801	119	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:28:49,269] [INFO] GTDB search result was written to OceanDNA-b31429/result_gtdb.tsv
[2023-03-17 05:28:49,269] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:28:49,272] [INFO] DFAST_QC result json was written to OceanDNA-b31429/dqc_result.json
[2023-03-17 05:28:49,272] [INFO] DFAST_QC completed!
[2023-03-17 05:28:49,272] [INFO] Total running time: 0h2m3s