[2023-06-27 11:31:11,742] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:31:11,744] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:31:11,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference
[2023-06-27 11:31:12,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:31:12,851] [INFO] Task started: Prodigal
[2023-06-27 11:31:12,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg18b7506f-44c6-4045-8a53-2691cee5ca01/GCA_026417015.1_ASM2641701v1_genomic.fna.gz | prodigal -d GCA_026417015.1_ASM2641701v1_genomic.fna/cds.fna -a GCA_026417015.1_ASM2641701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:31:17,137] [INFO] Task succeeded: Prodigal
[2023-06-27 11:31:17,138] [INFO] Task started: HMMsearch
[2023-06-27 11:31:17,138] [INFO] Running command: hmmsearch --tblout GCA_026417015.1_ASM2641701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference/reference_markers.hmm GCA_026417015.1_ASM2641701v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:31:17,301] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:31:17,302] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg18b7506f-44c6-4045-8a53-2691cee5ca01/GCA_026417015.1_ASM2641701v1_genomic.fna.gz]
[2023-06-27 11:31:17,324] [INFO] Query marker FASTA was written to GCA_026417015.1_ASM2641701v1_genomic.fna/markers.fasta
[2023-06-27 11:31:17,324] [INFO] Task started: Blastn
[2023-06-27 11:31:17,324] [INFO] Running command: blastn -query GCA_026417015.1_ASM2641701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference/reference_markers.fasta -out GCA_026417015.1_ASM2641701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:31:17,820] [INFO] Task succeeded: Blastn
[2023-06-27 11:31:17,823] [INFO] Selected 19 target genomes.
[2023-06-27 11:31:17,824] [INFO] Target genome list was writen to GCA_026417015.1_ASM2641701v1_genomic.fna/target_genomes.txt
[2023-06-27 11:31:17,833] [INFO] Task started: fastANI
[2023-06-27 11:31:17,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b7506f-44c6-4045-8a53-2691cee5ca01/GCA_026417015.1_ASM2641701v1_genomic.fna.gz --refList GCA_026417015.1_ASM2641701v1_genomic.fna/target_genomes.txt --output GCA_026417015.1_ASM2641701v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:31:35,661] [INFO] Task succeeded: fastANI
[2023-06-27 11:31:35,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:31:35,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:31:35,671] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:31:35,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:31:35,671] [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
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	76.3271	69	408	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	76.0414	80	408	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	75.9685	57	408	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	75.9089	78	408	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	75.8543	87	408	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	75.8341	87	408	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	75.82	57	408	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	75.7215	57	408	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	75.4647	54	408	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	75.4153	63	408	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	75.3798	82	408	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	75.3759	83	408	95	below_threshold
Burkholderia gladioli	strain=NCTC12378	GCA_900446225.1	28095	28095	type	True	75.3645	81	408	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:31:35,673] [INFO] DFAST Taxonomy check result was written to GCA_026417015.1_ASM2641701v1_genomic.fna/tc_result.tsv
[2023-06-27 11:31:35,674] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:31:35,674] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:31:35,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference/checkm_data
[2023-06-27 11:31:35,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:31:35,697] [INFO] Task started: CheckM
[2023-06-27 11:31:35,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026417015.1_ASM2641701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026417015.1_ASM2641701v1_genomic.fna/checkm_input GCA_026417015.1_ASM2641701v1_genomic.fna/checkm_result
[2023-06-27 11:31:53,085] [INFO] Task succeeded: CheckM
[2023-06-27 11:31:53,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:31:53,100] [INFO] ===== Completeness check finished =====
[2023-06-27 11:31:53,101] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:31:53,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026417015.1_ASM2641701v1_genomic.fna/markers.fasta)
[2023-06-27 11:31:53,102] [INFO] Task started: Blastn
[2023-06-27 11:31:53,102] [INFO] Running command: blastn -query GCA_026417015.1_ASM2641701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06fb139f-19ef-46fd-ba14-499735464841/dqc_reference/reference_markers_gtdb.fasta -out GCA_026417015.1_ASM2641701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:31:53,933] [INFO] Task succeeded: Blastn
[2023-06-27 11:31:53,936] [INFO] Selected 17 target genomes.
[2023-06-27 11:31:53,936] [INFO] Target genome list was writen to GCA_026417015.1_ASM2641701v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:31:53,959] [INFO] Task started: fastANI
[2023-06-27 11:31:53,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b7506f-44c6-4045-8a53-2691cee5ca01/GCA_026417015.1_ASM2641701v1_genomic.fna.gz --refList GCA_026417015.1_ASM2641701v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026417015.1_ASM2641701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:32:08,314] [INFO] Task succeeded: fastANI
[2023-06-27 11:32:08,323] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:32:08,323] [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
GCA_011056935.1	s__DSNY01 sp011056935	77.6163	162	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	98.37	98.37	0.91	0.91	2	-
GCA_016861185.1	s__DSNY01 sp016861185	77.3536	154	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632125.1	s__Cupriavidus cauae	76.3271	69	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.88	98.88	0.93	0.93	2	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	76.1356	74	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_007829435.1	s__Cupriavidus gilardii_D	76.0421	53	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426345.1	s__Cupriavidus sp000426345	75.9687	68	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.93	98.88	0.87	0.86	3	-
GCF_017814975.1	s__Cupriavidus sp017814975	75.9505	67	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069785.1	s__Cupriavidus taiwanensis	75.8878	86	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCA_016720425.1	s__CAIWHR01 sp016720425	75.7664	59	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCF_001580545.1	s__Paraburkholderia monticola	75.5007	52	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017104645.1	s__Burkholderia sp017104645	75.4719	64	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001524625.2	s__Burkholderia sp001524625	75.4454	64	408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.38	99.33	0.93	0.91	11	-
--------------------------------------------------------------------------------
[2023-06-27 11:32:08,326] [INFO] GTDB search result was written to GCA_026417015.1_ASM2641701v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:32:08,326] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:32:08,330] [INFO] DFAST_QC result json was written to GCA_026417015.1_ASM2641701v1_genomic.fna/dqc_result.json
[2023-06-27 11:32:08,330] [INFO] DFAST_QC completed!
[2023-06-27 11:32:08,330] [INFO] Total running time: 0h0m57s