[2024-01-24 10:47:54,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fac4f4b-d3a7-41e1-827a-97560ad74689/GCF_028472825.1_ASM2847282v1_genomic.fna.gz | prodigal -d GCF_028472825.1_ASM2847282v1_genomic.fna/cds.fna -a GCF_028472825.1_ASM2847282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:16,024] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:16,025] [INFO] Task started: HMMsearch
[2024-01-24 10:48:16,025] [INFO] Running command: hmmsearch --tblout GCF_028472825.1_ASM2847282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference/reference_markers.hmm GCF_028472825.1_ASM2847282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:16,320] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:16,321] [INFO] Found 6/6 markers.
[2024-01-24 10:48:16,366] [INFO] Query marker FASTA was written to GCF_028472825.1_ASM2847282v1_genomic.fna/markers.fasta
[2024-01-24 10:48:16,367] [INFO] Task started: Blastn
[2024-01-24 10:48:16,367] [INFO] Running command: blastn -query GCF_028472825.1_ASM2847282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference/reference_markers.fasta -out GCF_028472825.1_ASM2847282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:17,063] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:17,070] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:17,071] [INFO] Target genome list was writen to GCF_028472825.1_ASM2847282v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:17,154] [INFO] Task started: fastANI
[2024-01-24 10:48:17,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fac4f4b-d3a7-41e1-827a-97560ad74689/GCF_028472825.1_ASM2847282v1_genomic.fna.gz --refList GCF_028472825.1_ASM2847282v1_genomic.fna/target_genomes.txt --output GCF_028472825.1_ASM2847282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:33,962] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:33,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:33,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:33,987] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:33,987] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:33,988] [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 mediterranea	strain=MMB-1	GCA_000192865.1	119864	119864	type	True	99.9926	1559	1570	95	conclusive
Marinomonas balearica	strain=CECT 7378	GCA_004362145.1	491947	491947	type	True	84.3378	756	1570	95	below_threshold
Marinomonas aquiplantarum	strain=CECT 7732	GCA_003314975.1	491951	491951	type	True	79.6534	205	1570	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	79.3895	185	1570	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	79.339	178	1570	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	78.8011	176	1570	95	below_threshold
Marinomonas communis	strain=DSM 5604	GCA_004363305.1	28254	28254	type	True	78.7949	162	1570	95	below_threshold
Maribrevibacterium harenarium	strain=HB171799	GCA_006385675.1	2589817	2589817	type	True	78.7859	133	1570	95	below_threshold
Marinomonas ostreistagni	strain=UST010306-043	GCA_016888445.1	359209	359209	type	True	78.6636	136	1570	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	78.5594	170	1570	95	below_threshold
Marinomonas spartinae	strain=CECT 8886	GCA_900089775.1	1792290	1792290	type	True	78.4413	148	1570	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	78.412	188	1570	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001517305.1	1137284	1137284	type	True	78.4034	167	1570	95	below_threshold
Marinomonas fungiae	strain=JCM 18476	GCA_001418205.1	1137284	1137284	type	True	78.386	166	1570	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	78.1867	178	1570	95	below_threshold
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	78.0716	180	1570	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	77.8989	152	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:33,989] [INFO] DFAST Taxonomy check result was written to GCF_028472825.1_ASM2847282v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:33,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:33,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:33,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference/checkm_data
[2024-01-24 10:48:33,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:34,048] [INFO] Task started: CheckM
[2024-01-24 10:48:34,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028472825.1_ASM2847282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028472825.1_ASM2847282v1_genomic.fna/checkm_input GCF_028472825.1_ASM2847282v1_genomic.fna/checkm_result
[2024-01-24 10:49:15,899] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:15,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:15,923] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:15,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:15,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028472825.1_ASM2847282v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:15,924] [INFO] Task started: Blastn
[2024-01-24 10:49:15,925] [INFO] Running command: blastn -query GCF_028472825.1_ASM2847282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a991aa8-f684-4dbb-a6f0-919b5ac95017/dqc_reference/reference_markers_gtdb.fasta -out GCF_028472825.1_ASM2847282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:16,966] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:16,970] [INFO] Selected 20 target genomes.
[2024-01-24 10:49:16,970] [INFO] Target genome list was writen to GCF_028472825.1_ASM2847282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:16,985] [INFO] Task started: fastANI
[2024-01-24 10:49:16,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fac4f4b-d3a7-41e1-827a-97560ad74689/GCF_028472825.1_ASM2847282v1_genomic.fna.gz --refList GCF_028472825.1_ASM2847282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028472825.1_ASM2847282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:32,024] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:32,036] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:32,037] [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_000192865.1	s__Marinomonas mediterranea	99.9926	1560	1570	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_004362145.1	s__Marinomonas balearica	84.3277	757	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314975.1	s__Marinomonas aquiplantarum	79.6659	204	1570	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	79.4015	182	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013372285.1	s__Marinomonas primoryensis	79.0775	177	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
GCF_000017285.1	s__Marinomonas sp000017285	79.0083	184	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_006385675.1	s__Marinomonas sp006385675	78.8217	130	1570	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	78.7813	161	1570	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	78.7242	133	1570	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	78.6134	163	1570	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	78.4906	173	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_900129155.1	s__Marinomonas polaris	78.4023	188	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_001624705.1	s__Marinomonas sp001624705	78.3766	139	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.65	97.30	0.96	0.92	3	-
GCF_001418205.1	s__Marinomonas fungiae	78.3509	164	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259225.1	s__Marinomonas arctica	78.1614	178	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014803385.1	s__Marinomonas colpomeniae	77.893	150	1570	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 10:49:32,084] [INFO] GTDB search result was written to GCF_028472825.1_ASM2847282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:32,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:32,091] [INFO] DFAST_QC result json was written to GCF_028472825.1_ASM2847282v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:32,091] [INFO] DFAST_QC completed!
[2024-01-24 10:49:32,091] [INFO] Total running time: 0h1m38s