[2024-01-24 11:59:12,953] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,955] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,955] [INFO] DQC Reference Directory: /var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference
[2024-01-24 11:59:14,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,324] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4710b6e-5a66-4b28-87c2-96e8daf858e8/GCF_014652655.1_ASM1465265v1_genomic.fna.gz | prodigal -d GCF_014652655.1_ASM1465265v1_genomic.fna/cds.fna -a GCF_014652655.1_ASM1465265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:25,568] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:25,569] [INFO] Task started: HMMsearch
[2024-01-24 11:59:25,569] [INFO] Running command: hmmsearch --tblout GCF_014652655.1_ASM1465265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference/reference_markers.hmm GCF_014652655.1_ASM1465265v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:25,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:25,861] [INFO] Found 6/6 markers.
[2024-01-24 11:59:25,907] [INFO] Query marker FASTA was written to GCF_014652655.1_ASM1465265v1_genomic.fna/markers.fasta
[2024-01-24 11:59:25,907] [INFO] Task started: Blastn
[2024-01-24 11:59:25,907] [INFO] Running command: blastn -query GCF_014652655.1_ASM1465265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference/reference_markers.fasta -out GCF_014652655.1_ASM1465265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:26,619] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:26,622] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:26,623] [INFO] Target genome list was writen to GCF_014652655.1_ASM1465265v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:26,631] [INFO] Task started: fastANI
[2024-01-24 11:59:26,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4710b6e-5a66-4b28-87c2-96e8daf858e8/GCF_014652655.1_ASM1465265v1_genomic.fna.gz --refList GCF_014652655.1_ASM1465265v1_genomic.fna/target_genomes.txt --output GCF_014652655.1_ASM1465265v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:38,362] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:38,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:38,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:38,373] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:38,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:38,374] [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
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	100.0	1043	1044	95	conclusive
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	89.1059	857	1044	95	below_threshold
Nereida ignava	strain=CECT 5292	GCA_001049735.1	282199	282199	type	True	76.6646	52	1044	95	below_threshold
Nereida ignava	strain=DSM 16309	GCA_900114125.1	282199	282199	type	True	76.6559	54	1044	95	below_threshold
Nereida ignava	strain=CECT 5292	GCA_001404155.1	282199	282199	type	True	76.6241	53	1044	95	below_threshold
Falsihalocynthiibacter arcticus	strain=PAMC 20958	GCA_000812665.2	1579316	1579316	type	True	76.4623	62	1044	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.3122	72	1044	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.2715	54	1044	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	76.0856	55	1044	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.0594	57	1044	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:38,379] [INFO] DFAST Taxonomy check result was written to GCF_014652655.1_ASM1465265v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:38,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:38,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:38,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference/checkm_data
[2024-01-24 11:59:38,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:38,446] [INFO] Task started: CheckM
[2024-01-24 11:59:38,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652655.1_ASM1465265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652655.1_ASM1465265v1_genomic.fna/checkm_input GCF_014652655.1_ASM1465265v1_genomic.fna/checkm_result
[2024-01-24 12:00:16,603] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:16,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:16,624] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:16,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:16,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652655.1_ASM1465265v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:16,625] [INFO] Task started: Blastn
[2024-01-24 12:00:16,625] [INFO] Running command: blastn -query GCF_014652655.1_ASM1465265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef11725-1f6c-4e74-abe8-9cc5ef1470b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652655.1_ASM1465265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:18,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:18,488] [INFO] Selected 18 target genomes.
[2024-01-24 12:00:18,488] [INFO] Target genome list was writen to GCF_014652655.1_ASM1465265v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:18,504] [INFO] Task started: fastANI
[2024-01-24 12:00:18,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4710b6e-5a66-4b28-87c2-96e8daf858e8/GCF_014652655.1_ASM1465265v1_genomic.fna.gz --refList GCF_014652655.1_ASM1465265v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652655.1_ASM1465265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:28,245] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:28,256] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:28,256] [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_014652655.1	s__Amylibacter ulvae	100.0	1043	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002742285.1	s__Amylibacter kogurei	89.1059	857	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184395.1	s__Amylibacter sp009184395	77.8486	134	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469545.1	s__Amylibacter sp002469545	77.0356	102	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401045.1	s__Amylibacter sp002401045	76.8309	66	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764475.1	s__Amylibacter sp016764475	76.7716	110	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001049735.1	s__Nereida ignava	76.6626	52	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nereida	95.0	99.99	99.98	0.99	0.99	3	-
GCF_002150005.2	s__Marivivens niveibacter	76.4977	75	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	76.2816	71	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706605.1	s__SAT37 sp002706605	76.1558	63	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCA_017854855.1	s__Sulfitobacter sp017854855	75.6562	52	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	75.5549	66	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:28,257] [INFO] GTDB search result was written to GCF_014652655.1_ASM1465265v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:28,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:28,263] [INFO] DFAST_QC result json was written to GCF_014652655.1_ASM1465265v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:28,263] [INFO] DFAST_QC completed!
[2024-01-24 12:00:28,263] [INFO] Total running time: 0h1m15s