[2024-01-24 13:25:31,216] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,220] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference
[2024-01-24 13:25:32,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,598] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c79ea1b-3512-4136-9c04-dfcb0d55bcfd/GCF_004352835.1_ASM435283v1_genomic.fna.gz | prodigal -d GCF_004352835.1_ASM435283v1_genomic.fna/cds.fna -a GCF_004352835.1_ASM435283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:41,179] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:41,179] [INFO] Task started: HMMsearch
[2024-01-24 13:25:41,180] [INFO] Running command: hmmsearch --tblout GCF_004352835.1_ASM435283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference/reference_markers.hmm GCF_004352835.1_ASM435283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:41,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:41,462] [INFO] Found 6/6 markers.
[2024-01-24 13:25:41,495] [INFO] Query marker FASTA was written to GCF_004352835.1_ASM435283v1_genomic.fna/markers.fasta
[2024-01-24 13:25:41,495] [INFO] Task started: Blastn
[2024-01-24 13:25:41,495] [INFO] Running command: blastn -query GCF_004352835.1_ASM435283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference/reference_markers.fasta -out GCF_004352835.1_ASM435283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:42,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:42,209] [INFO] Selected 19 target genomes.
[2024-01-24 13:25:42,210] [INFO] Target genome list was writen to GCF_004352835.1_ASM435283v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:42,215] [INFO] Task started: fastANI
[2024-01-24 13:25:42,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c79ea1b-3512-4136-9c04-dfcb0d55bcfd/GCF_004352835.1_ASM435283v1_genomic.fna.gz --refList GCF_004352835.1_ASM435283v1_genomic.fna/target_genomes.txt --output GCF_004352835.1_ASM435283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:56,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:56,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:56,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:56,083] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:56,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:56,083] [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 flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	100.0	1236	1236	95	conclusive
Marinomonas pollencensis	strain=CECT 7375	GCA_003387375.1	491954	491954	type	True	81.2032	642	1236	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	79.2643	355	1236	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	79.1618	320	1236	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	79.1577	347	1236	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	79.1046	329	1236	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	79.0548	333	1236	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	79.0468	334	1236	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	79.0255	343	1236	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	79.003	374	1236	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	78.921	330	1236	95	below_threshold
Marinomonas ushuaiensis	strain=DSM 15871	GCA_000521805.1	263818	263818	type	True	78.9083	337	1236	95	below_threshold
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	78.8598	335	1236	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	78.8157	337	1236	95	below_threshold
Marinomonas spartinae	strain=CECT 8886	GCA_900089775.1	1792290	1792290	type	True	78.7253	324	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:56,085] [INFO] DFAST Taxonomy check result was written to GCF_004352835.1_ASM435283v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:56,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:56,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:56,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference/checkm_data
[2024-01-24 13:25:56,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:56,137] [INFO] Task started: CheckM
[2024-01-24 13:25:56,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004352835.1_ASM435283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004352835.1_ASM435283v1_genomic.fna/checkm_input GCF_004352835.1_ASM435283v1_genomic.fna/checkm_result
[2024-01-24 13:26:26,778] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:26,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:26,803] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:26,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:26,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004352835.1_ASM435283v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:26,804] [INFO] Task started: Blastn
[2024-01-24 13:26:26,804] [INFO] Running command: blastn -query GCF_004352835.1_ASM435283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd660fa2-2838-409d-830a-db50ee0528e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004352835.1_ASM435283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:27,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:27,895] [INFO] Selected 17 target genomes.
[2024-01-24 13:26:27,895] [INFO] Target genome list was writen to GCF_004352835.1_ASM435283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:27,907] [INFO] Task started: fastANI
[2024-01-24 13:26:27,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c79ea1b-3512-4136-9c04-dfcb0d55bcfd/GCF_004352835.1_ASM435283v1_genomic.fna.gz --refList GCF_004352835.1_ASM435283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004352835.1_ASM435283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:40,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:40,335] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:40,335] [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_004352835.1	s__Marinomonas sp004352835	100.0	1236	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004352855.1	s__Marinomonas sp004352855	82.1522	759	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387375.1	s__Marinomonas pollencensis	81.1854	643	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208215.1	s__Marinomonas alcarazii	79.1715	319	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_000508165.1	s__Marinomonas profundimaris	79.1635	346	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018336955.1	s__Marinomonas sp018336955	79.124	360	1236	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	79.114	328	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
GCF_003315485.1	s__Marinomonas rhizomae	79.034	342	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012584435.1	s__Marinomonas sp012584435	78.9377	330	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259175.1	s__Marinomonas shanghaiensis	78.9082	325	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521805.1	s__Marinomonas ushuaiensis	78.8947	337	1236	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	78.8127	336	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900089775.1	s__Marinomonas spartinae	78.7316	323	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.99	98.99	0.93	0.93	2	-
GCF_016463975.1	s__Marinomonas sp016463975	78.6892	301	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461715.1	s__Marinomonas spartinae_A	78.5887	327	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639745.1	s__Marinomonas gallaica	77.6905	175	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.95	96.94	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:40,337] [INFO] GTDB search result was written to GCF_004352835.1_ASM435283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:40,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:40,342] [INFO] DFAST_QC result json was written to GCF_004352835.1_ASM435283v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:40,342] [INFO] DFAST_QC completed!
[2024-01-24 13:26:40,342] [INFO] Total running time: 0h1m9s