[2024-01-24 15:03:00,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:00,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:00,012] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference
[2024-01-24 15:03:01,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:01,348] [INFO] Task started: Prodigal
[2024-01-24 15:03:01,348] [INFO] Running command: gunzip -c /var/lib/cwl/stgef5ec736-4eb2-47ed-9fb9-d35733a8fe9a/GCF_014645175.1_ASM1464517v1_genomic.fna.gz | prodigal -d GCF_014645175.1_ASM1464517v1_genomic.fna/cds.fna -a GCF_014645175.1_ASM1464517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:13,337] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:13,338] [INFO] Task started: HMMsearch
[2024-01-24 15:03:13,338] [INFO] Running command: hmmsearch --tblout GCF_014645175.1_ASM1464517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference/reference_markers.hmm GCF_014645175.1_ASM1464517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:13,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:13,666] [INFO] Found 6/6 markers.
[2024-01-24 15:03:13,709] [INFO] Query marker FASTA was written to GCF_014645175.1_ASM1464517v1_genomic.fna/markers.fasta
[2024-01-24 15:03:13,709] [INFO] Task started: Blastn
[2024-01-24 15:03:13,709] [INFO] Running command: blastn -query GCF_014645175.1_ASM1464517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference/reference_markers.fasta -out GCF_014645175.1_ASM1464517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:14,463] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:14,467] [INFO] Selected 15 target genomes.
[2024-01-24 15:03:14,467] [INFO] Target genome list was writen to GCF_014645175.1_ASM1464517v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:14,474] [INFO] Task started: fastANI
[2024-01-24 15:03:14,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5ec736-4eb2-47ed-9fb9-d35733a8fe9a/GCF_014645175.1_ASM1464517v1_genomic.fna.gz --refList GCF_014645175.1_ASM1464517v1_genomic.fna/target_genomes.txt --output GCF_014645175.1_ASM1464517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:29,057] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:29,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:29,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:29,073] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:29,074] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:29,074] [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 arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	100.0	1460	1461	95	conclusive
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	99.9863	1424	1461	95	conclusive
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	87.8152	1157	1461	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	83.0513	989	1461	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	82.7943	927	1461	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	81.5729	804	1461	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	81.5669	778	1461	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	81.4927	810	1461	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	81.3703	797	1461	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	80.4187	666	1461	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	80.1249	710	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:29,076] [INFO] DFAST Taxonomy check result was written to GCF_014645175.1_ASM1464517v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:29,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:29,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:29,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference/checkm_data
[2024-01-24 15:03:29,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:29,124] [INFO] Task started: CheckM
[2024-01-24 15:03:29,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645175.1_ASM1464517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645175.1_ASM1464517v1_genomic.fna/checkm_input GCF_014645175.1_ASM1464517v1_genomic.fna/checkm_result
[2024-01-24 15:04:07,593] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:07,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:07,616] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:07,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:07,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645175.1_ASM1464517v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:07,617] [INFO] Task started: Blastn
[2024-01-24 15:04:07,617] [INFO] Running command: blastn -query GCF_014645175.1_ASM1464517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc0c6c48-692e-4104-b691-b7cf8deec4d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645175.1_ASM1464517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:08,714] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:08,718] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:08,719] [INFO] Target genome list was writen to GCF_014645175.1_ASM1464517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:08,729] [INFO] Task started: fastANI
[2024-01-24 15:04:08,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5ec736-4eb2-47ed-9fb9-d35733a8fe9a/GCF_014645175.1_ASM1464517v1_genomic.fna.gz --refList GCF_014645175.1_ASM1464517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645175.1_ASM1464517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:20,055] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:20,066] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:20,066] [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_003259225.1	s__Marinomonas arctica	99.9863	1424	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003259175.1	s__Marinomonas shanghaiensis	87.8037	1158	1461	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	83.0508	990	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_018336955.1	s__Marinomonas sp018336955	82.8205	936	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	82.2658	964	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_012584435.1	s__Marinomonas sp012584435	82.2164	807	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315485.1	s__Marinomonas rhizomae	81.5652	805	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003208215.1	s__Marinomonas alcarazii	81.5403	780	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_003337275.1	s__Marinomonas foliarum	81.3672	797	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_018336975.1	s__Marinomonas sp013373235	80.7605	780	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_016463975.1	s__Marinomonas sp016463975	78.891	452	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153025.1	s__Marinomonas sp000153025	77.7662	149	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:20,072] [INFO] GTDB search result was written to GCF_014645175.1_ASM1464517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:20,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:20,078] [INFO] DFAST_QC result json was written to GCF_014645175.1_ASM1464517v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:20,078] [INFO] DFAST_QC completed!
[2024-01-24 15:04:20,079] [INFO] Total running time: 0h1m20s