[2023-03-18 01:24:53,312] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:24:53,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:24:53,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference
[2023-03-18 01:24:54,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:24:54,419] [INFO] Task started: Prodigal
[2023-03-18 01:24:54,419] [INFO] Running command: cat /var/lib/cwl/stg46f0e06d-9e30-4f53-913d-cf173d37b23c/OceanDNA-b32981.fa | prodigal -d OceanDNA-b32981/cds.fna -a OceanDNA-b32981/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:25:20,283] [INFO] Task succeeded: Prodigal
[2023-03-18 01:25:20,284] [INFO] Task started: HMMsearch
[2023-03-18 01:25:20,284] [INFO] Running command: hmmsearch --tblout OceanDNA-b32981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference/reference_markers.hmm OceanDNA-b32981/protein.faa > /dev/null
[2023-03-18 01:25:20,498] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:25:20,499] [INFO] Found 6/6 markers.
[2023-03-18 01:25:20,523] [INFO] Query marker FASTA was written to OceanDNA-b32981/markers.fasta
[2023-03-18 01:25:20,524] [INFO] Task started: Blastn
[2023-03-18 01:25:20,524] [INFO] Running command: blastn -query OceanDNA-b32981/markers.fasta -db /var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference/reference_markers.fasta -out OceanDNA-b32981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:21,290] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:21,291] [INFO] Selected 30 target genomes.
[2023-03-18 01:25:21,291] [INFO] Target genome list was writen to OceanDNA-b32981/target_genomes.txt
[2023-03-18 01:25:21,392] [INFO] Task started: fastANI
[2023-03-18 01:25:21,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg46f0e06d-9e30-4f53-913d-cf173d37b23c/OceanDNA-b32981.fa --refList OceanDNA-b32981/target_genomes.txt --output OceanDNA-b32981/fastani_result.tsv --threads 1
[2023-03-18 01:25:43,026] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:43,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:25:43,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:25:43,038] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:25:43,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:25:43,038] [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
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	77.9256	407	1363	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	76.293	158	1363	95	below_threshold
Aestuariispira ectoiniformans	strain=SWCN16	GCA_025136295.1	2775080	2775080	type	True	76.1982	118	1363	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1333	112	1363	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1285	99	1363	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.0798	101	1363	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.008	111	1363	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.9883	91	1363	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.9823	113	1363	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9527	96	1363	95	below_threshold
Aestuariispira insulae	strain=CECT 8488	GCA_003385955.1	1461337	1461337	type	True	75.9209	74	1363	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.7428	78	1363	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	75.6977	50	1363	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	75.6438	65	1363	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	75.6318	61	1363	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.6282	108	1363	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.6085	83	1363	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.6049	64	1363	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	75.5648	121	1363	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	75.3296	60	1363	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:25:43,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32981/tc_result.tsv
[2023-03-18 01:25:43,039] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:25:43,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:25:43,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference/checkm_data
[2023-03-18 01:25:43,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:25:43,045] [INFO] Task started: CheckM
[2023-03-18 01:25:43,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32981/checkm_input OceanDNA-b32981/checkm_result
[2023-03-18 01:26:46,186] [INFO] Task succeeded: CheckM
[2023-03-18 01:26:46,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:26:46,189] [INFO] ===== Completeness check finished =====
[2023-03-18 01:26:46,189] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:26:46,190] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32981/markers.fasta)
[2023-03-18 01:26:46,191] [INFO] Task started: Blastn
[2023-03-18 01:26:46,191] [INFO] Running command: blastn -query OceanDNA-b32981/markers.fasta -db /var/lib/cwl/stg650e1ec4-2f32-4c70-a3f3-5fd34f06f904/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:47,605] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:47,607] [INFO] Selected 20 target genomes.
[2023-03-18 01:26:47,607] [INFO] Target genome list was writen to OceanDNA-b32981/target_genomes_gtdb.txt
[2023-03-18 01:26:47,693] [INFO] Task started: fastANI
[2023-03-18 01:26:47,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg46f0e06d-9e30-4f53-913d-cf173d37b23c/OceanDNA-b32981.fa --refList OceanDNA-b32981/target_genomes_gtdb.txt --output OceanDNA-b32981/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:01,031] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:01,039] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:27:01,039] [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_017792345.1	s__GCA-2696645 sp017792345	78.2183	504	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCA_012926505.1	s__GCA-2696645 sp012926505	77.918	408	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017963645.1	s__Marivibrio halodurans	76.5886	207	1363	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_002709955.1	s__GCA-2696645 sp002709955	76.5711	228	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.86	99.71	0.96	0.91	10	-
GCA_002696645.1	s__GCA-2696645 sp002696645	76.4498	198	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.85	99.85	0.96	0.96	2	-
GCA_017640745.1	s__Nisaea sp017640745	76.1186	96	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523655.1	s__Bin65 sp011523655	76.0424	81	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	95.25	95.16	0.87	0.83	5	-
GCA_002727315.1	s__UBA8079 sp002727315	75.9344	54	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	75.8743	81	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667335.1	s__UBA8079 sp018667335	75.7902	54	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCF_000333275.1	s__Nitrospirillum sp000333275	75.52	68	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	75.3296	60	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:01,039] [INFO] GTDB search result was written to OceanDNA-b32981/result_gtdb.tsv
[2023-03-18 01:27:01,039] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:01,041] [INFO] DFAST_QC result json was written to OceanDNA-b32981/dqc_result.json
[2023-03-18 01:27:01,041] [INFO] DFAST_QC completed!
[2023-03-18 01:27:01,041] [INFO] Total running time: 0h2m8s