[2023-03-18 08:17:20,561] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,562] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference
[2023-03-18 08:17:21,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,731] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,731] [INFO] Running command: cat /var/lib/cwl/stgc55aed86-573c-4231-ba72-9f2ab61b09c4/OceanDNA-b23306.fa | prodigal -d OceanDNA-b23306/cds.fna -a OceanDNA-b23306/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:36,621] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:36,622] [INFO] Task started: HMMsearch
[2023-03-18 08:17:36,622] [INFO] Running command: hmmsearch --tblout OceanDNA-b23306/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference/reference_markers.hmm OceanDNA-b23306/protein.faa > /dev/null
[2023-03-18 08:17:36,901] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:36,901] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc55aed86-573c-4231-ba72-9f2ab61b09c4/OceanDNA-b23306.fa]
[2023-03-18 08:17:36,926] [INFO] Query marker FASTA was written to OceanDNA-b23306/markers.fasta
[2023-03-18 08:17:36,926] [INFO] Task started: Blastn
[2023-03-18 08:17:36,926] [INFO] Running command: blastn -query OceanDNA-b23306/markers.fasta -db /var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference/reference_markers.fasta -out OceanDNA-b23306/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:37,589] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:37,590] [INFO] Selected 23 target genomes.
[2023-03-18 08:17:37,590] [INFO] Target genome list was writen to OceanDNA-b23306/target_genomes.txt
[2023-03-18 08:17:37,605] [INFO] Task started: fastANI
[2023-03-18 08:17:37,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55aed86-573c-4231-ba72-9f2ab61b09c4/OceanDNA-b23306.fa --refList OceanDNA-b23306/target_genomes.txt --output OceanDNA-b23306/fastani_result.tsv --threads 1
[2023-03-18 08:17:55,105] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:55,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:55,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:55,117] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:55,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:55,117] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.3306	147	664	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.2323	85	664	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.2205	130	664	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2131	91	664	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.0035	109	664	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.9361	70	664	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.9106	119	664	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.8986	96	664	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8852	141	664	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.8663	140	664	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.8623	139	664	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.8317	107	664	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.6757	83	664	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.6221	71	664	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.577	65	664	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	75.5137	60	664	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.4934	71	664	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	75.3841	53	664	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	75.3812	70	664	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	75.3636	52	664	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	75.1049	51	664	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:55,117] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23306/tc_result.tsv
[2023-03-18 08:17:55,117] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:55,117] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:55,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference/checkm_data
[2023-03-18 08:17:55,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:55,123] [INFO] Task started: CheckM
[2023-03-18 08:17:55,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23306/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23306/checkm_input OceanDNA-b23306/checkm_result
[2023-03-18 08:18:34,767] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:34,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:34,771] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:34,771] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:34,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23306/markers.fasta)
[2023-03-18 08:18:34,771] [INFO] Task started: Blastn
[2023-03-18 08:18:34,771] [INFO] Running command: blastn -query OceanDNA-b23306/markers.fasta -db /var/lib/cwl/stg5efa817d-16c1-46bd-936d-4139644430c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23306/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:35,811] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:35,812] [INFO] Selected 25 target genomes.
[2023-03-18 08:18:35,812] [INFO] Target genome list was writen to OceanDNA-b23306/target_genomes_gtdb.txt
[2023-03-18 08:18:35,834] [INFO] Task started: fastANI
[2023-03-18 08:18:35,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55aed86-573c-4231-ba72-9f2ab61b09c4/OceanDNA-b23306.fa --refList OceanDNA-b23306/target_genomes_gtdb.txt --output OceanDNA-b23306/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:52,746] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:52,758] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:52,758] [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_014652915.1	s__Thalassobaculum_A fulvum	76.2943	150	664	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_002148795.1	s__Oceanibaculum nanhaiense	76.2324	85	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.2314	90	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.0183	108	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	75.9853	101	664	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_001657395.1	s__Pelagibius sp001657395	75.949	85	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	75.9317	82	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869175.1	s__VGEV01 sp016869175	75.8733	84	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__VGEV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.856	140	664	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_002937115.1	s__Rhodopila globiformis	75.7746	92	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	75.7445	104	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	75.6757	83	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	75.5839	76	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794075.1	s__SYSU-D60009 sp016794075	75.5549	68	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60009	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694185.1	s__SHVR01 sp009694185	75.5278	69	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVR01;f__SHVR01;g__SHVR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	75.4222	59	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128965.1	s__Roseomonas_C arctica	75.3912	54	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.3883	90	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	75.3731	86	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_000802185.1	s__Belnapia sp000802185	75.295	95	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	75.1167	50	664	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:52,758] [INFO] GTDB search result was written to OceanDNA-b23306/result_gtdb.tsv
[2023-03-18 08:18:52,758] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:52,761] [INFO] DFAST_QC result json was written to OceanDNA-b23306/dqc_result.json
[2023-03-18 08:18:52,761] [INFO] DFAST_QC completed!
[2023-03-18 08:18:52,761] [INFO] Total running time: 0h1m32s