[2023-06-17 05:59:54,181] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:59:54,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:59:54,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference
[2023-06-17 05:59:55,474] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:59:55,474] [INFO] Task started: Prodigal
[2023-06-17 05:59:55,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fac10d3-5aaf-4367-a50b-9b0065ed5891/GCA_009360795.1_ASM936079v1_genomic.fna.gz | prodigal -d GCA_009360795.1_ASM936079v1_genomic.fna/cds.fna -a GCA_009360795.1_ASM936079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:00:08,895] [INFO] Task succeeded: Prodigal
[2023-06-17 06:00:08,896] [INFO] Task started: HMMsearch
[2023-06-17 06:00:08,896] [INFO] Running command: hmmsearch --tblout GCA_009360795.1_ASM936079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference/reference_markers.hmm GCA_009360795.1_ASM936079v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:00:09,176] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:00:09,178] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2fac10d3-5aaf-4367-a50b-9b0065ed5891/GCA_009360795.1_ASM936079v1_genomic.fna.gz]
[2023-06-17 06:00:09,225] [INFO] Query marker FASTA was written to GCA_009360795.1_ASM936079v1_genomic.fna/markers.fasta
[2023-06-17 06:00:09,226] [INFO] Task started: Blastn
[2023-06-17 06:00:09,226] [INFO] Running command: blastn -query GCA_009360795.1_ASM936079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference/reference_markers.fasta -out GCA_009360795.1_ASM936079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:00:09,806] [INFO] Task succeeded: Blastn
[2023-06-17 06:00:09,810] [INFO] Selected 9 target genomes.
[2023-06-17 06:00:09,810] [INFO] Target genome list was writen to GCA_009360795.1_ASM936079v1_genomic.fna/target_genomes.txt
[2023-06-17 06:00:09,816] [INFO] Task started: fastANI
[2023-06-17 06:00:09,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fac10d3-5aaf-4367-a50b-9b0065ed5891/GCA_009360795.1_ASM936079v1_genomic.fna.gz --refList GCA_009360795.1_ASM936079v1_genomic.fna/target_genomes.txt --output GCA_009360795.1_ASM936079v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:00:23,311] [INFO] Task succeeded: fastANI
[2023-06-17 06:00:23,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:00:23,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:00:23,320] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2023-06-17 06:00:23,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 06:00:23,320] [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 denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	98.6726	1272	1420	95	conclusive
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	98.6335	1283	1420	95	conclusive
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	98.6128	1270	1420	95	conclusive
Achromobacter denitrificans	strain=NCTC8582	GCA_900444675.1	32002	32002	type	True	98.6123	1265	1420	95	conclusive
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	90.2649	1090	1420	95	below_threshold
Achromobacter agilis	strain=LMG 3411	GCA_900496965.1	1353888	1353888	type	True	89.5439	1069	1420	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	85.3419	909	1420	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	84.9965	835	1420	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	84.8497	915	1420	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:00:23,323] [INFO] DFAST Taxonomy check result was written to GCA_009360795.1_ASM936079v1_genomic.fna/tc_result.tsv
[2023-06-17 06:00:23,324] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:00:23,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:00:23,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference/checkm_data
[2023-06-17 06:00:23,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:00:23,380] [INFO] Task started: CheckM
[2023-06-17 06:00:23,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009360795.1_ASM936079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009360795.1_ASM936079v1_genomic.fna/checkm_input GCA_009360795.1_ASM936079v1_genomic.fna/checkm_result
[2023-06-17 06:01:04,548] [INFO] Task succeeded: CheckM
[2023-06-17 06:01:04,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:01:04,576] [INFO] ===== Completeness check finished =====
[2023-06-17 06:01:04,576] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:01:04,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009360795.1_ASM936079v1_genomic.fna/markers.fasta)
[2023-06-17 06:01:04,577] [INFO] Task started: Blastn
[2023-06-17 06:01:04,577] [INFO] Running command: blastn -query GCA_009360795.1_ASM936079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg813eb14b-9de4-47e3-af53-5351b94f3913/dqc_reference/reference_markers_gtdb.fasta -out GCA_009360795.1_ASM936079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:01:05,238] [INFO] Task succeeded: Blastn
[2023-06-17 06:01:05,261] [INFO] Selected 13 target genomes.
[2023-06-17 06:01:05,261] [INFO] Target genome list was writen to GCA_009360795.1_ASM936079v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:01:05,292] [INFO] Task started: fastANI
[2023-06-17 06:01:05,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fac10d3-5aaf-4367-a50b-9b0065ed5891/GCA_009360795.1_ASM936079v1_genomic.fna.gz --refList GCA_009360795.1_ASM936079v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009360795.1_ASM936079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:01:22,308] [INFO] Task succeeded: fastANI
[2023-06-17 06:01:22,323] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:01:22,324] [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_001571365.1	s__Achromobacter denitrificans	98.6103	1271	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	conclusive
GCF_900496975.1	s__Achromobacter veterisilvae	90.2647	1091	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900496965.1	s__Achromobacter agilis	89.5489	1068	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757485.1	s__Achromobacter sp000757485	89.1951	1079	1420	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	87.5619	932	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_902859735.1	s__Achromobacter aegrifaciens	86.9732	1012	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_902859645.1	s__Achromobacter insuavis	85.7211	890	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_016127315.1	s__Achromobacter insuavis_A	85.5207	918	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_001457475.1	s__Achromobacter xylosoxidans	85.3655	907	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_902859765.1	s__Achromobacter pulmonis	84.9893	836	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
GCF_002975275.1	s__Achromobacter sp002975275	84.9426	929	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859705.1	s__Achromobacter deleyi	84.8949	911	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.99	97.40	0.95	0.91	5	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.441	71	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-17 06:01:22,327] [INFO] GTDB search result was written to GCA_009360795.1_ASM936079v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:01:22,327] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:01:22,331] [INFO] DFAST_QC result json was written to GCA_009360795.1_ASM936079v1_genomic.fna/dqc_result.json
[2023-06-17 06:01:22,331] [INFO] DFAST_QC completed!
[2023-06-17 06:01:22,331] [INFO] Total running time: 0h1m28s