[2024-01-24 12:13:26,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:26,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:26,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference
[2024-01-24 12:13:28,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:28,154] [INFO] Task started: Prodigal
[2024-01-24 12:13:28,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c67dc50-5c46-4cb8-acec-4d2cf9399ad6/GCF_006385675.1_ASM638567v1_genomic.fna.gz | prodigal -d GCF_006385675.1_ASM638567v1_genomic.fna/cds.fna -a GCF_006385675.1_ASM638567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:39,788] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:39,789] [INFO] Task started: HMMsearch
[2024-01-24 12:13:39,789] [INFO] Running command: hmmsearch --tblout GCF_006385675.1_ASM638567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference/reference_markers.hmm GCF_006385675.1_ASM638567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:40,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:40,069] [INFO] Found 6/6 markers.
[2024-01-24 12:13:40,103] [INFO] Query marker FASTA was written to GCF_006385675.1_ASM638567v1_genomic.fna/markers.fasta
[2024-01-24 12:13:40,103] [INFO] Task started: Blastn
[2024-01-24 12:13:40,103] [INFO] Running command: blastn -query GCF_006385675.1_ASM638567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference/reference_markers.fasta -out GCF_006385675.1_ASM638567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:40,845] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:40,848] [INFO] Selected 22 target genomes.
[2024-01-24 12:13:40,848] [INFO] Target genome list was writen to GCF_006385675.1_ASM638567v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:40,863] [INFO] Task started: fastANI
[2024-01-24 12:13:40,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c67dc50-5c46-4cb8-acec-4d2cf9399ad6/GCF_006385675.1_ASM638567v1_genomic.fna.gz --refList GCF_006385675.1_ASM638567v1_genomic.fna/target_genomes.txt --output GCF_006385675.1_ASM638567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,086] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:55,098] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:55,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:55,099] [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
Maribrevibacterium harenarium	strain=HB171799	GCA_006385675.1	2589817	2589817	type	True	100.0	1161	1167	95	conclusive
Marinomonas fungiae	strain=JCM 18476	GCA_001517305.1	1137284	1137284	type	True	80.5706	271	1167	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001418205.1	1137284	1137284	type	True	80.5645	272	1167	95	below_threshold
Marinomonas aquimarina	strain=11SM4	GCA_001639695.1	295068	295068	type	True	80.0889	251	1167	95	below_threshold
Marinomonas aquimarina	strain=CECT 5080	GCA_900089755.1	295068	295068	type	True	80.0745	254	1167	95	below_threshold
Marinomonas pollencensis	strain=CECT 7375	GCA_003387375.1	491954	491954	type	True	79.9224	149	1167	95	below_threshold
Marinomonas communis	strain=DSM 5604	GCA_004363305.1	28254	28254	type	True	79.281	244	1167	95	below_threshold
Marinomonas ostreistagni	strain=UST010306-043	GCA_016888445.1	359209	359209	type	True	79.0695	214	1167	95	below_threshold
Marinomonas balearica	strain=CECT 7378	GCA_004362145.1	491947	491947	type	True	78.7451	113	1167	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	78.4104	162	1167	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	78.1096	152	1167	95	below_threshold
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	78.0602	135	1167	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	77.4416	114	1167	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	77.429	127	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:55,101] [INFO] DFAST Taxonomy check result was written to GCF_006385675.1_ASM638567v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:55,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:55,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:55,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference/checkm_data
[2024-01-24 12:13:55,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:55,140] [INFO] Task started: CheckM
[2024-01-24 12:13:55,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385675.1_ASM638567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385675.1_ASM638567v1_genomic.fna/checkm_input GCF_006385675.1_ASM638567v1_genomic.fna/checkm_result
[2024-01-24 12:14:33,049] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:33,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:33,077] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:33,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:33,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385675.1_ASM638567v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:33,079] [INFO] Task started: Blastn
[2024-01-24 12:14:33,079] [INFO] Running command: blastn -query GCF_006385675.1_ASM638567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4397201e-4225-466e-9165-4441d5d2d448/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385675.1_ASM638567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:34,249] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:34,255] [INFO] Selected 20 target genomes.
[2024-01-24 12:14:34,255] [INFO] Target genome list was writen to GCF_006385675.1_ASM638567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:34,293] [INFO] Task started: fastANI
[2024-01-24 12:14:34,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c67dc50-5c46-4cb8-acec-4d2cf9399ad6/GCF_006385675.1_ASM638567v1_genomic.fna.gz --refList GCF_006385675.1_ASM638567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385675.1_ASM638567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:48,226] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:48,240] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:48,240] [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_006385675.1	s__Marinomonas sp006385675	100.0	1161	1167	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_001418205.1	s__Marinomonas fungiae	80.5645	272	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900089755.1	s__Marinomonas aquimarina	80.0745	254	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003387375.1	s__Marinomonas pollencensis	79.89	150	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461785.1	s__Marinomonas ostreistagni_A	79.4893	217	1167	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	79.281	244	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.16	97.04	0.89	0.87	3	-
GCF_016888445.1	s__Marinomonas ostreistagni	79.0509	215	1167	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	78.4518	128	1167	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	78.4104	162	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_003259225.1	s__Marinomonas arctica	78.3023	147	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003208215.1	s__Marinomonas alcarazii	78.0898	153	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_004352835.1	s__Marinomonas sp004352835	78.0602	135	1167	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	78.0355	152	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_014803385.1	s__Marinomonas colpomeniae	77.4416	114	1167	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	77.429	127	1167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:48,242] [INFO] GTDB search result was written to GCF_006385675.1_ASM638567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:48,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:48,247] [INFO] DFAST_QC result json was written to GCF_006385675.1_ASM638567v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:48,248] [INFO] DFAST_QC completed!
[2024-01-24 12:14:48,248] [INFO] Total running time: 0h1m21s