[2023-03-15 16:25:56,995] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,003] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,003] [INFO] DQC Reference Directory: /var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference
[2023-03-15 16:25:58,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,595] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,595] [INFO] Running command: cat /var/lib/cwl/stgb94fb2bd-07e5-4cfc-9fde-29c478595e45/OceanDNA-b38495.fa | prodigal -d OceanDNA-b38495/cds.fna -a OceanDNA-b38495/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:12,479] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:12,479] [INFO] Task started: HMMsearch
[2023-03-15 16:26:12,480] [INFO] Running command: hmmsearch --tblout OceanDNA-b38495/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference/reference_markers.hmm OceanDNA-b38495/protein.faa > /dev/null
[2023-03-15 16:26:12,695] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:12,696] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb94fb2bd-07e5-4cfc-9fde-29c478595e45/OceanDNA-b38495.fa]
[2023-03-15 16:26:12,787] [INFO] Query marker FASTA was written to OceanDNA-b38495/markers.fasta
[2023-03-15 16:26:12,788] [INFO] Task started: Blastn
[2023-03-15 16:26:12,788] [INFO] Running command: blastn -query OceanDNA-b38495/markers.fasta -db /var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference/reference_markers.fasta -out OceanDNA-b38495/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:13,349] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:13,358] [INFO] Selected 24 target genomes.
[2023-03-15 16:26:13,359] [INFO] Target genome list was writen to OceanDNA-b38495/target_genomes.txt
[2023-03-15 16:26:13,374] [INFO] Task started: fastANI
[2023-03-15 16:26:13,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgb94fb2bd-07e5-4cfc-9fde-29c478595e45/OceanDNA-b38495.fa --refList OceanDNA-b38495/target_genomes.txt --output OceanDNA-b38495/fastani_result.tsv --threads 1
[2023-03-15 16:26:28,073] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:28,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:28,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:28,082] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:28,083] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:26:28,083] [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
Marinomonas vulgaris	strain=A79	GCA_018145875.1	2823372	2823372	type	True	78.2862	64	836	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	78.2412	75	836	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	78.1498	88	836	95	below_threshold
Marinomonas pollencensis	strain=CECT 7375	GCA_003387375.1	491954	491954	type	True	78.0478	88	836	95	below_threshold
Marinomonas aquiplantarum	strain=CECT 7732	GCA_003314975.1	491951	491951	type	True	78.0155	83	836	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	78.0032	76	836	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	77.9849	79	836	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	77.9398	91	836	95	below_threshold
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	77.9326	82	836	95	below_threshold
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	77.9125	80	836	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	77.7369	101	836	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	77.6928	82	836	95	below_threshold
Marinomonas ushuaiensis	strain=DSM 15871	GCA_000521805.1	263818	263818	type	True	77.4627	95	836	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:26:28,087] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38495/tc_result.tsv
[2023-03-15 16:26:28,096] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:28,096] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:28,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference/checkm_data
[2023-03-15 16:26:28,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:28,109] [INFO] Task started: CheckM
[2023-03-15 16:26:28,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38495/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38495/checkm_input OceanDNA-b38495/checkm_result
[2023-03-15 16:27:06,624] [INFO] Task succeeded: CheckM
[2023-03-15 16:27:06,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:27:06,704] [INFO] ===== Completeness check finished =====
[2023-03-15 16:27:06,704] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:27:06,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38495/markers.fasta)
[2023-03-15 16:27:06,706] [INFO] Task started: Blastn
[2023-03-15 16:27:06,706] [INFO] Running command: blastn -query OceanDNA-b38495/markers.fasta -db /var/lib/cwl/stga49beb77-4bb4-4e86-9ff0-3075772c89b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38495/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:27:07,576] [INFO] Task succeeded: Blastn
[2023-03-15 16:27:07,585] [INFO] Selected 20 target genomes.
[2023-03-15 16:27:07,586] [INFO] Target genome list was writen to OceanDNA-b38495/target_genomes_gtdb.txt
[2023-03-15 16:27:07,620] [INFO] Task started: fastANI
[2023-03-15 16:27:07,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgb94fb2bd-07e5-4cfc-9fde-29c478595e45/OceanDNA-b38495.fa --refList OceanDNA-b38495/target_genomes_gtdb.txt --output OceanDNA-b38495/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:27:19,853] [INFO] Task succeeded: fastANI
[2023-03-15 16:27:19,861] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:27:19,862] [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_001624705.1	s__Marinomonas sp001624705	82.7079	567	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.65	97.30	0.96	0.92	3	-
GCF_000153025.1	s__Marinomonas sp000153025	81.5601	497	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372285.1	s__Marinomonas primoryensis	78.2591	74	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
GCF_003208215.1	s__Marinomonas alcarazii	78.1639	87	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_003387375.1	s__Marinomonas pollencensis	78.0478	88	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508165.1	s__Marinomonas profundimaris	78.0032	76	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259225.1	s__Marinomonas arctica	77.9985	78	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_018336955.1	s__Marinomonas sp018336955	77.9533	90	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352835.1	s__Marinomonas sp004352835	77.9232	81	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129155.1	s__Marinomonas polaris	77.7451	100	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_014803385.1	s__Marinomonas colpomeniae	77.6928	82	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018336975.1	s__Marinomonas sp013373235	77.4882	96	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_000521805.1	s__Marinomonas ushuaiensis	77.4685	94	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002173415.2	s__Marinomonas agarivorans	76.8395	73	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:27:19,865] [INFO] GTDB search result was written to OceanDNA-b38495/result_gtdb.tsv
[2023-03-15 16:27:19,870] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:27:19,876] [INFO] DFAST_QC result json was written to OceanDNA-b38495/dqc_result.json
[2023-03-15 16:27:19,876] [INFO] DFAST_QC completed!
[2023-03-15 16:27:19,876] [INFO] Total running time: 0h1m23s