[2023-03-16 17:47:09,010] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:47:09,011] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:47:09,011] [INFO] DQC Reference Directory: /var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference
[2023-03-16 17:47:10,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:47:10,097] [INFO] Task started: Prodigal
[2023-03-16 17:47:10,097] [INFO] Running command: cat /var/lib/cwl/stg3fd2ebc4-b7b0-4824-80fd-db1f23bb9f5d/OceanDNA-b30013.fa | prodigal -d OceanDNA-b30013/cds.fna -a OceanDNA-b30013/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:47:37,508] [INFO] Task succeeded: Prodigal
[2023-03-16 17:47:37,508] [INFO] Task started: HMMsearch
[2023-03-16 17:47:37,508] [INFO] Running command: hmmsearch --tblout OceanDNA-b30013/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference/reference_markers.hmm OceanDNA-b30013/protein.faa > /dev/null
[2023-03-16 17:47:38,013] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:47:38,014] [INFO] Found 6/6 markers.
[2023-03-16 17:47:38,048] [INFO] Query marker FASTA was written to OceanDNA-b30013/markers.fasta
[2023-03-16 17:47:38,054] [INFO] Task started: Blastn
[2023-03-16 17:47:38,054] [INFO] Running command: blastn -query OceanDNA-b30013/markers.fasta -db /var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference/reference_markers.fasta -out OceanDNA-b30013/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:47:39,896] [INFO] Task succeeded: Blastn
[2023-03-16 17:47:39,897] [INFO] Selected 23 target genomes.
[2023-03-16 17:47:39,897] [INFO] Target genome list was writen to OceanDNA-b30013/target_genomes.txt
[2023-03-16 17:47:39,933] [INFO] Task started: fastANI
[2023-03-16 17:47:39,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fd2ebc4-b7b0-4824-80fd-db1f23bb9f5d/OceanDNA-b30013.fa --refList OceanDNA-b30013/target_genomes.txt --output OceanDNA-b30013/fastani_result.tsv --threads 1
[2023-03-16 17:48:01,066] [INFO] Task succeeded: fastANI
[2023-03-16 17:48:01,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:48:01,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:48:01,080] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:48:01,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:48:01,080] [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
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.6046	563	1075	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	79.3093	546	1075	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.2862	553	1075	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.2195	402	1075	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.2012	403	1075	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.1768	337	1075	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.1719	377	1075	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.1615	322	1075	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1557	336	1075	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.0501	331	1075	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.9854	334	1075	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.9589	348	1075	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	77.9106	323	1075	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.9082	335	1075	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.8454	303	1075	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.5742	274	1075	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.5345	287	1075	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.3925	299	1075	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.3602	302	1075	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.0528	221	1075	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.9068	229	1075	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.8872	214	1075	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7198	152	1075	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:48:01,080] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30013/tc_result.tsv
[2023-03-16 17:48:01,081] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:48:01,081] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:48:01,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference/checkm_data
[2023-03-16 17:48:01,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:48:01,086] [INFO] Task started: CheckM
[2023-03-16 17:48:01,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30013/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30013/checkm_input OceanDNA-b30013/checkm_result
[2023-03-16 17:49:04,950] [INFO] Task succeeded: CheckM
[2023-03-16 17:49:04,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:49:04,953] [INFO] ===== Completeness check finished =====
[2023-03-16 17:49:04,953] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:49:04,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30013/markers.fasta)
[2023-03-16 17:49:04,954] [INFO] Task started: Blastn
[2023-03-16 17:49:04,954] [INFO] Running command: blastn -query OceanDNA-b30013/markers.fasta -db /var/lib/cwl/stgbee9a107-978a-461d-b9d3-3c28f471ee19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30013/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:49:06,407] [INFO] Task succeeded: Blastn
[2023-03-16 17:49:06,407] [INFO] Selected 14 target genomes.
[2023-03-16 17:49:06,407] [INFO] Target genome list was writen to OceanDNA-b30013/target_genomes_gtdb.txt
[2023-03-16 17:49:06,438] [INFO] Task started: fastANI
[2023-03-16 17:49:06,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fd2ebc4-b7b0-4824-80fd-db1f23bb9f5d/OceanDNA-b30013.fa --refList OceanDNA-b30013/target_genomes_gtdb.txt --output OceanDNA-b30013/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:49:18,485] [INFO] Task succeeded: fastANI
[2023-03-16 17:49:18,494] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:49:18,494] [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_002709085.1	s__Pseudooceanicola sp002709085	98.2579	827	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004959925.1	s__Pseudooceanicola onchidii	79.6134	562	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	79.5436	581	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	79.3752	552	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	79.3207	549	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	79.1587	554	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_900109145.1	s__Marinovum algicola	78.333	317	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.2011	403	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	78.1816	376	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.1812	357	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003590145.2	s__Pseudooceanicola algae	78.1508	323	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003575965.1	s__Pseudooceanicola sediminis	77.9211	322	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCA_001650895.1	s__EhC02 sp001650895	77.7646	302	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	77.7014	324	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:49:18,494] [INFO] GTDB search result was written to OceanDNA-b30013/result_gtdb.tsv
[2023-03-16 17:49:18,494] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:49:18,496] [INFO] DFAST_QC result json was written to OceanDNA-b30013/dqc_result.json
[2023-03-16 17:49:18,496] [INFO] DFAST_QC completed!
[2023-03-16 17:49:18,496] [INFO] Total running time: 0h2m9s