[2023-03-14 13:28:15,848] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:28:15,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:28:15,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference
[2023-03-14 13:28:16,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:28:16,986] [INFO] Task started: Prodigal
[2023-03-14 13:28:16,986] [INFO] Running command: cat /var/lib/cwl/stg25176f64-1dbb-4221-9752-abe8e030561f/OceanDNA-b29472.fa | prodigal -d OceanDNA-b29472/cds.fna -a OceanDNA-b29472/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:28:39,631] [INFO] Task succeeded: Prodigal
[2023-03-14 13:28:39,631] [INFO] Task started: HMMsearch
[2023-03-14 13:28:39,631] [INFO] Running command: hmmsearch --tblout OceanDNA-b29472/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference/reference_markers.hmm OceanDNA-b29472/protein.faa > /dev/null
[2023-03-14 13:28:40,018] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:28:40,019] [INFO] Found 6/6 markers.
[2023-03-14 13:28:40,039] [INFO] Query marker FASTA was written to OceanDNA-b29472/markers.fasta
[2023-03-14 13:28:40,046] [INFO] Task started: Blastn
[2023-03-14 13:28:40,046] [INFO] Running command: blastn -query OceanDNA-b29472/markers.fasta -db /var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference/reference_markers.fasta -out OceanDNA-b29472/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:28:41,595] [INFO] Task succeeded: Blastn
[2023-03-14 13:28:41,596] [INFO] Selected 28 target genomes.
[2023-03-14 13:28:41,596] [INFO] Target genome list was writen to OceanDNA-b29472/target_genomes.txt
[2023-03-14 13:28:41,612] [INFO] Task started: fastANI
[2023-03-14 13:28:41,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg25176f64-1dbb-4221-9752-abe8e030561f/OceanDNA-b29472.fa --refList OceanDNA-b29472/target_genomes.txt --output OceanDNA-b29472/fastani_result.tsv --threads 1
[2023-03-14 13:29:03,927] [INFO] Task succeeded: fastANI
[2023-03-14 13:29:03,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:29:03,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:29:03,942] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 13:29:03,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 13:29:03,943] [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
Lentibacter algarum	strain=DSM 24677	GCA_900107355.1	576131	576131	type	True	99.5897	945	1003	95	conclusive
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.0974	145	1003	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	76.935	105	1003	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	76.6837	90	1003	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.6725	123	1003	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	76.5733	113	1003	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	76.5376	113	1003	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.4714	82	1003	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.4712	104	1003	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	76.4193	110	1003	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3924	129	1003	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.3744	92	1003	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.3669	103	1003	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3517	129	1003	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	76.2972	110	1003	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.2837	102	1003	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.2835	113	1003	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.2653	114	1003	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	76.2408	105	1003	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.2106	97	1003	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.2054	66	1003	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.197	89	1003	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	76.1635	111	1003	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.0846	88	1003	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	75.9278	114	1003	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	75.6715	51	1003	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.5852	65	1003	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	75.5282	51	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:29:03,943] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29472/tc_result.tsv
[2023-03-14 13:29:03,943] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:29:03,943] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:29:03,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference/checkm_data
[2023-03-14 13:29:03,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:29:04,008] [INFO] Task started: CheckM
[2023-03-14 13:29:04,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29472/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29472/checkm_input OceanDNA-b29472/checkm_result
[2023-03-14 13:29:53,721] [INFO] Task succeeded: CheckM
[2023-03-14 13:29:53,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:29:53,724] [INFO] ===== Completeness check finished =====
[2023-03-14 13:29:53,724] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:29:53,724] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29472/markers.fasta)
[2023-03-14 13:29:53,725] [INFO] Task started: Blastn
[2023-03-14 13:29:53,725] [INFO] Running command: blastn -query OceanDNA-b29472/markers.fasta -db /var/lib/cwl/stg3733614b-0965-463c-8c5a-b0a1410074ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29472/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:29:55,029] [INFO] Task succeeded: Blastn
[2023-03-14 13:29:55,030] [INFO] Selected 18 target genomes.
[2023-03-14 13:29:55,030] [INFO] Target genome list was writen to OceanDNA-b29472/target_genomes_gtdb.txt
[2023-03-14 13:29:55,037] [INFO] Task started: fastANI
[2023-03-14 13:29:55,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg25176f64-1dbb-4221-9752-abe8e030561f/OceanDNA-b29472.fa --refList OceanDNA-b29472/target_genomes_gtdb.txt --output OceanDNA-b29472/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:30:07,727] [INFO] Task succeeded: fastANI
[2023-03-14 13:30:07,738] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:30:07,738] [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_900107355.1	s__Lentibacter algarum	99.5897	945	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018500075.1	s__Lentibacter sp018500075	83.0992	598	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744435.1	s__Lentibacter sp016744435	77.8716	350	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860975.1	s__Lentibacter algarum_A	77.845	323	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003417655.1	s__Lentibacter sp003417655	77.2447	261	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.0974	145	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004645.1	s__Aliiroseovarius halocynthiae	76.6837	90	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.5291	165	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	76.3622	123	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	76.345	117	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768555.3	s__Roseovarius mucosus	76.2924	109	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	76.2917	127	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900188035.1	s__Puniceibacterium sediminis	76.2888	114	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	76.256	116	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	76.2417	118	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_900109855.1	s__Roseovarius tolerans	76.1635	111	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_900109035.1	s__Cribrihabitans marinus	76.0744	87	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	75.9278	114	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:30:07,739] [INFO] GTDB search result was written to OceanDNA-b29472/result_gtdb.tsv
[2023-03-14 13:30:07,739] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:30:07,742] [INFO] DFAST_QC result json was written to OceanDNA-b29472/dqc_result.json
[2023-03-14 13:30:07,742] [INFO] DFAST_QC completed!
[2023-03-14 13:30:07,742] [INFO] Total running time: 0h1m52s