[2024-01-24 13:49:18,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:18,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:18,835] [INFO] DQC Reference Directory: /var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference
[2024-01-24 13:49:20,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,275] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,276] [INFO] Running command: gunzip -c /var/lib/cwl/stg58faefe2-d6cc-44b6-8377-31925901d4d8/GCF_004614185.1_ASM461418v1_genomic.fna.gz | prodigal -d GCF_004614185.1_ASM461418v1_genomic.fna/cds.fna -a GCF_004614185.1_ASM461418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:36,508] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:36,508] [INFO] Task started: HMMsearch
[2024-01-24 13:49:36,508] [INFO] Running command: hmmsearch --tblout GCF_004614185.1_ASM461418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference/reference_markers.hmm GCF_004614185.1_ASM461418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:36,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:36,820] [INFO] Found 6/6 markers.
[2024-01-24 13:49:36,873] [INFO] Query marker FASTA was written to GCF_004614185.1_ASM461418v1_genomic.fna/markers.fasta
[2024-01-24 13:49:36,874] [INFO] Task started: Blastn
[2024-01-24 13:49:36,874] [INFO] Running command: blastn -query GCF_004614185.1_ASM461418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference/reference_markers.fasta -out GCF_004614185.1_ASM461418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:37,990] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:37,999] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:37,999] [INFO] Target genome list was writen to GCF_004614185.1_ASM461418v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:38,005] [INFO] Task started: fastANI
[2024-01-24 13:49:38,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg58faefe2-d6cc-44b6-8377-31925901d4d8/GCF_004614185.1_ASM461418v1_genomic.fna.gz --refList GCF_004614185.1_ASM461418v1_genomic.fna/target_genomes.txt --output GCF_004614185.1_ASM461418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,182] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:58,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,182] [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
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	100.0	1522	1534	95	conclusive
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.4964	845	1534	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	81.4663	849	1534	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.3993	853	1534	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.3943	716	1534	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	81.2179	863	1534	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	81.1808	863	1534	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.1533	860	1534	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	80.9802	735	1534	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	80.9396	744	1534	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	80.8275	767	1534	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	80.7769	835	1534	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	80.7592	784	1534	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	80.7347	834	1534	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	80.4065	752	1534	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	80.1469	814	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,184] [INFO] DFAST Taxonomy check result was written to GCF_004614185.1_ASM461418v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference/checkm_data
[2024-01-24 13:49:58,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,237] [INFO] Task started: CheckM
[2024-01-24 13:49:58,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004614185.1_ASM461418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004614185.1_ASM461418v1_genomic.fna/checkm_input GCF_004614185.1_ASM461418v1_genomic.fna/checkm_result
[2024-01-24 13:50:45,567] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:45,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,587] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:45,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:45,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004614185.1_ASM461418v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:45,588] [INFO] Task started: Blastn
[2024-01-24 13:50:45,588] [INFO] Running command: blastn -query GCF_004614185.1_ASM461418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3872db0-5d1b-471e-931e-1f19fce31e28/dqc_reference/reference_markers_gtdb.fasta -out GCF_004614185.1_ASM461418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:47,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:47,716] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:47,716] [INFO] Target genome list was writen to GCF_004614185.1_ASM461418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:47,774] [INFO] Task started: fastANI
[2024-01-24 13:50:47,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg58faefe2-d6cc-44b6-8377-31925901d4d8/GCF_004614185.1_ASM461418v1_genomic.fna.gz --refList GCF_004614185.1_ASM461418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004614185.1_ASM461418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:14,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:14,962] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:14,962] [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_004614185.1	s__Massilia arenosa	100.0	1522	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002007115.1	s__Massilia sp002007115	81.6166	848	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003484545.1	s__Massilia sp003484545	81.5092	575	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119395.1	s__Massilia sp018119395	81.4727	853	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_003590855.1	s__Massilia sp003590855	81.3973	715	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119405.1	s__Massilia sp018119405	81.3779	857	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116645.1	s__Pseudoduganella namucuonensis	81.238	855	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	81.2116	865	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427785.1	s__Massilia alkalitolerans	81.0725	859	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_006715485.1	s__Massilia sp006715485	80.9611	844	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745265.1	s__Massilia sp000745265	80.9521	814	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053665.1	s__Pseudoduganella sp003053665	80.9429	846	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.77	95.97	0.96	0.89	5	-
GCF_004614195.1	s__Massilia horti	80.9421	743	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425265.1	s__Pseudoduganella sp001425265	80.9233	840	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849555.1	s__Massilia sp012849555	80.8278	887	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003953935.1	s__Massilia atriviolacea	80.7594	837	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857595.1	s__Pseudoduganella aquatica_A	80.7487	832	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461825.1	s__Rugamonas sp016461825	80.568	815	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001191005.1	s__Pseudoduganella sp001191005	80.4716	757	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	80.3026	731	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322755.1	s__Pseudoduganella albidiflava	80.1085	787	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:14,963] [INFO] GTDB search result was written to GCF_004614185.1_ASM461418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:14,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:14,968] [INFO] DFAST_QC result json was written to GCF_004614185.1_ASM461418v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:14,968] [INFO] DFAST_QC completed!
[2024-01-24 13:51:14,968] [INFO] Total running time: 0h1m56s