[2024-01-24 13:17:33,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,342] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference
[2024-01-24 13:17:34,653] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:34,655] [INFO] Task started: Prodigal
[2024-01-24 13:17:34,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e574440-4ccd-4cc2-a7b7-c04a726c366d/GCF_004362145.1_ASM436214v1_genomic.fna.gz | prodigal -d GCF_004362145.1_ASM436214v1_genomic.fna/cds.fna -a GCF_004362145.1_ASM436214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:43,756] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:43,756] [INFO] Task started: HMMsearch
[2024-01-24 13:17:43,756] [INFO] Running command: hmmsearch --tblout GCF_004362145.1_ASM436214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference/reference_markers.hmm GCF_004362145.1_ASM436214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:44,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:44,024] [INFO] Found 6/6 markers.
[2024-01-24 13:17:44,057] [INFO] Query marker FASTA was written to GCF_004362145.1_ASM436214v1_genomic.fna/markers.fasta
[2024-01-24 13:17:44,057] [INFO] Task started: Blastn
[2024-01-24 13:17:44,058] [INFO] Running command: blastn -query GCF_004362145.1_ASM436214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference/reference_markers.fasta -out GCF_004362145.1_ASM436214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:44,723] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:44,726] [INFO] Selected 21 target genomes.
[2024-01-24 13:17:44,726] [INFO] Target genome list was writen to GCF_004362145.1_ASM436214v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:44,734] [INFO] Task started: fastANI
[2024-01-24 13:17:44,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e574440-4ccd-4cc2-a7b7-c04a726c366d/GCF_004362145.1_ASM436214v1_genomic.fna.gz --refList GCF_004362145.1_ASM436214v1_genomic.fna/target_genomes.txt --output GCF_004362145.1_ASM436214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:00,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:00,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:00,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:00,951] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:00,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:00,952] [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 balearica	strain=CECT 7378	GCA_004362145.1	491947	491947	type	True	100.0	1285	1285	95	conclusive
Marinomonas mediterranea	strain=MMB-1	GCA_000192865.1	119864	119864	type	True	84.2432	791	1285	95	below_threshold
Marinomonas aquimarina	strain=CECT 5080	GCA_900089755.1	295068	295068	type	True	79.0742	125	1285	95	below_threshold
Maribrevibacterium harenarium	strain=HB171799	GCA_006385675.1	2589817	2589817	type	True	78.8953	119	1285	95	below_threshold
Marinomonas aquimarina	strain=11SM4	GCA_001639695.1	295068	295068	type	True	78.8622	130	1285	95	below_threshold
Marinomonas communis	strain=DSM 5604	GCA_004363305.1	28254	28254	type	True	78.8415	156	1285	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001517305.1	1137284	1137284	type	True	78.5352	139	1285	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001418205.1	1137284	1137284	type	True	78.5352	139	1285	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	78.4986	159	1285	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	78.369	154	1285	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	78.2201	168	1285	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	78.1055	151	1285	95	below_threshold
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	78.0557	153	1285	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	78.0517	150	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:00,953] [INFO] DFAST Taxonomy check result was written to GCF_004362145.1_ASM436214v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:00,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:00,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:00,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference/checkm_data
[2024-01-24 13:18:00,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:00,993] [INFO] Task started: CheckM
[2024-01-24 13:18:00,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362145.1_ASM436214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362145.1_ASM436214v1_genomic.fna/checkm_input GCF_004362145.1_ASM436214v1_genomic.fna/checkm_result
[2024-01-24 13:18:34,675] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:34,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,691] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:34,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:34,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362145.1_ASM436214v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:34,693] [INFO] Task started: Blastn
[2024-01-24 13:18:34,693] [INFO] Running command: blastn -query GCF_004362145.1_ASM436214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5b718f0-7297-4383-980d-fb6f2be309c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362145.1_ASM436214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:35,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:35,769] [INFO] Selected 19 target genomes.
[2024-01-24 13:18:35,770] [INFO] Target genome list was writen to GCF_004362145.1_ASM436214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:35,784] [INFO] Task started: fastANI
[2024-01-24 13:18:35,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e574440-4ccd-4cc2-a7b7-c04a726c366d/GCF_004362145.1_ASM436214v1_genomic.fna.gz --refList GCF_004362145.1_ASM436214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362145.1_ASM436214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:49,621] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:49,663] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:49,664] [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_004362145.1	s__Marinomonas balearica	100.0	1285	1285	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_000192865.1	s__Marinomonas mediterranea	84.2562	790	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089755.1	s__Marinomonas aquimarina	79.0637	124	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385675.1	s__Marinomonas sp006385675	78.9289	119	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363305.1	s__Marinomonas communis	78.8219	155	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.16	97.04	0.89	0.87	3	-
GCF_003208215.1	s__Marinomonas alcarazii	78.5004	160	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_000017285.1	s__Marinomonas sp000017285	78.4989	164	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_001418205.1	s__Marinomonas fungiae	78.4879	139	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337275.1	s__Marinomonas foliarum	78.349	154	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_001624705.1	s__Marinomonas sp001624705	78.3307	127	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.65	97.30	0.96	0.92	3	-
GCF_900129155.1	s__Marinomonas polaris	78.2201	168	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_003259175.1	s__Marinomonas shanghaiensis	78.1055	151	1285	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	78.0527	152	1285	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	78.0525	150	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
GCF_008122525.1	s__Marinomonas sp008122525	77.9386	130	1285	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	77.7946	78	1285	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 13:18:49,665] [INFO] GTDB search result was written to GCF_004362145.1_ASM436214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:49,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:49,670] [INFO] DFAST_QC result json was written to GCF_004362145.1_ASM436214v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:49,670] [INFO] DFAST_QC completed!
[2024-01-24 13:18:49,670] [INFO] Total running time: 0h1m16s