[2024-01-24 12:29:28,641] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference
[2024-01-24 12:29:29,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,932] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg0aa03985-27c3-4cd5-b99f-e34f3e42e2c2/GCF_003315095.1_ASM331509v1_genomic.fna.gz | prodigal -d GCF_003315095.1_ASM331509v1_genomic.fna/cds.fna -a GCF_003315095.1_ASM331509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:56,715] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:56,715] [INFO] Task started: HMMsearch
[2024-01-24 12:29:56,716] [INFO] Running command: hmmsearch --tblout GCF_003315095.1_ASM331509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference/reference_markers.hmm GCF_003315095.1_ASM331509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:57,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:57,154] [INFO] Found 6/6 markers.
[2024-01-24 12:29:57,211] [INFO] Query marker FASTA was written to GCF_003315095.1_ASM331509v1_genomic.fna/markers.fasta
[2024-01-24 12:29:57,211] [INFO] Task started: Blastn
[2024-01-24 12:29:57,211] [INFO] Running command: blastn -query GCF_003315095.1_ASM331509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference/reference_markers.fasta -out GCF_003315095.1_ASM331509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:58,227] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:58,232] [INFO] Selected 19 target genomes.
[2024-01-24 12:29:58,233] [INFO] Target genome list was writen to GCF_003315095.1_ASM331509v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:58,241] [INFO] Task started: fastANI
[2024-01-24 12:29:58,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa03985-27c3-4cd5-b99f-e34f3e42e2c2/GCF_003315095.1_ASM331509v1_genomic.fna.gz --refList GCF_003315095.1_ASM331509v1_genomic.fna/target_genomes.txt --output GCF_003315095.1_ASM331509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:25,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:25,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:25,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:25,169] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:30:25,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:25,170] [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
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	100.0	2271	2272	95	conclusive
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	99.9956	2260	2272	95	conclusive
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	99.9943	2254	2272	95	conclusive
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	88.5713	1793	2272	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.7344	1737	2272	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	87.1983	1596	2272	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	86.7773	1638	2272	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	86.6285	1478	2272	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	86.044	1600	2272	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.5563	1590	2272	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	85.3226	1534	2272	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.8458	865	2272	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.8296	345	2272	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	77.6839	379	2272	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.3849	292	2272	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	77.2267	430	2272	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	75.8657	149	2272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:25,172] [INFO] DFAST Taxonomy check result was written to GCF_003315095.1_ASM331509v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:25,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:25,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:25,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference/checkm_data
[2024-01-24 12:30:25,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:25,249] [INFO] Task started: CheckM
[2024-01-24 12:30:25,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315095.1_ASM331509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315095.1_ASM331509v1_genomic.fna/checkm_input GCF_003315095.1_ASM331509v1_genomic.fna/checkm_result
[2024-01-24 12:31:38,705] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:38,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:38,728] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:38,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:38,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315095.1_ASM331509v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:38,729] [INFO] Task started: Blastn
[2024-01-24 12:31:38,729] [INFO] Running command: blastn -query GCF_003315095.1_ASM331509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc193c85-778f-4cb7-b6ee-12e52c425741/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315095.1_ASM331509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:40,510] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:40,516] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:40,516] [INFO] Target genome list was writen to GCF_003315095.1_ASM331509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:40,526] [INFO] Task started: fastANI
[2024-01-24 12:31:40,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa03985-27c3-4cd5-b99f-e34f3e42e2c2/GCF_003315095.1_ASM331509v1_genomic.fna.gz --refList GCF_003315095.1_ASM331509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315095.1_ASM331509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:00,172] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:00,187] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:00,187] [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_002209535.1	s__Achromobacter marplatensis	99.9956	2260	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.15	97.44	0.96	0.90	4	conclusive
GCF_012928505.1	s__Achromobacter sp012928505	91.7607	1811	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170335.1	s__Achromobacter sp014170335	91.2049	1831	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975275.1	s__Achromobacter sp002975275	89.9138	1765	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859625.1	s__Achromobacter pestifer	88.5793	1792	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859595.1	s__Achromobacter kerstersii	87.7307	1738	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.61	98.61	0.95	0.95	2	-
GCF_013116765.2	s__Achromobacter deleyi_A	86.8877	1606	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600685.1	s__Achromobacter spanius_B	86.8209	1597	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.56	98.20	0.94	0.92	5	-
GCF_003994415.1	s__Achromobacter spanius_C	86.7653	1565	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.60	98.60	0.94	0.94	2	-
GCF_000236785.1	s__Achromobacter arsenitoxydans	86.1612	1488	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	85.9417	1428	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	75.847	153	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002068855.1	s__UBA1934 sp002068855	75.8026	79	2272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA1934	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:00,189] [INFO] GTDB search result was written to GCF_003315095.1_ASM331509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:00,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:00,193] [INFO] DFAST_QC result json was written to GCF_003315095.1_ASM331509v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:00,193] [INFO] DFAST_QC completed!
[2024-01-24 12:32:00,193] [INFO] Total running time: 0h2m32s