[2024-01-24 14:30:45,636] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,638] [INFO] DQC Reference Directory: /var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference
[2024-01-24 14:30:46,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,898] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f8c23ba-1a2f-4734-b837-19b17af6cafa/GCF_016809835.1_ASM1680983v2_genomic.fna.gz | prodigal -d GCF_016809835.1_ASM1680983v2_genomic.fna/cds.fna -a GCF_016809835.1_ASM1680983v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:02,760] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:02,760] [INFO] Task started: HMMsearch
[2024-01-24 14:31:02,761] [INFO] Running command: hmmsearch --tblout GCF_016809835.1_ASM1680983v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference/reference_markers.hmm GCF_016809835.1_ASM1680983v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:03,087] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:03,089] [INFO] Found 6/6 markers.
[2024-01-24 14:31:03,139] [INFO] Query marker FASTA was written to GCF_016809835.1_ASM1680983v2_genomic.fna/markers.fasta
[2024-01-24 14:31:03,140] [INFO] Task started: Blastn
[2024-01-24 14:31:03,140] [INFO] Running command: blastn -query GCF_016809835.1_ASM1680983v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference/reference_markers.fasta -out GCF_016809835.1_ASM1680983v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:04,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:04,272] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:04,272] [INFO] Target genome list was writen to GCF_016809835.1_ASM1680983v2_genomic.fna/target_genomes.txt
[2024-01-24 14:31:04,278] [INFO] Task started: fastANI
[2024-01-24 14:31:04,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f8c23ba-1a2f-4734-b837-19b17af6cafa/GCF_016809835.1_ASM1680983v2_genomic.fna.gz --refList GCF_016809835.1_ASM1680983v2_genomic.fna/target_genomes.txt --output GCF_016809835.1_ASM1680983v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:21,986] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:21,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:21,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:22,000] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:22,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:22,000] [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 soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	100.0	1648	1649	95	conclusive
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	87.8517	1195	1649	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	85.1625	999	1649	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	82.6837	1027	1649	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.5899	1036	1649	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	82.4673	972	1649	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	82.4318	981	1649	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	82.3707	1031	1649	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	82.1778	1012	1649	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.6922	855	1649	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.6576	878	1649	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.3774	943	1649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:22,002] [INFO] DFAST Taxonomy check result was written to GCF_016809835.1_ASM1680983v2_genomic.fna/tc_result.tsv
[2024-01-24 14:31:22,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:22,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:22,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference/checkm_data
[2024-01-24 14:31:22,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:22,055] [INFO] Task started: CheckM
[2024-01-24 14:31:22,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016809835.1_ASM1680983v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016809835.1_ASM1680983v2_genomic.fna/checkm_input GCF_016809835.1_ASM1680983v2_genomic.fna/checkm_result
[2024-01-24 14:32:10,105] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:10,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:10,131] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:10,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:10,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016809835.1_ASM1680983v2_genomic.fna/markers.fasta)
[2024-01-24 14:32:10,132] [INFO] Task started: Blastn
[2024-01-24 14:32:10,132] [INFO] Running command: blastn -query GCF_016809835.1_ASM1680983v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge65f6783-6509-48f1-bdd0-8cfc236b40ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_016809835.1_ASM1680983v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:12,367] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:12,371] [INFO] Selected 16 target genomes.
[2024-01-24 14:32:12,371] [INFO] Target genome list was writen to GCF_016809835.1_ASM1680983v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:12,391] [INFO] Task started: fastANI
[2024-01-24 14:32:12,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f8c23ba-1a2f-4734-b837-19b17af6cafa/GCF_016809835.1_ASM1680983v2_genomic.fna.gz --refList GCF_016809835.1_ASM1680983v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016809835.1_ASM1680983v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:34,332] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:34,345] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:32:34,345] [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_012927275.1	s__Massilia sp012927275	87.8625	1194	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	85.186	999	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760655.1	s__Massilia eurypsychrophila	82.701	1024	1649	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	82.6142	1033	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	82.4945	969	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682175.1	s__Massilia frigida	82.4494	979	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	82.4219	1012	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682145.1	s__Massilia mucilaginosa	82.382	1030	1649	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	82.2889	617	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	82.1659	1012	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCA_002428015.1	s__Massilia sp002428015	82.1548	900	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689335.1	s__Massilia sp001485665	82.1172	1007	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.10	97.10	0.90	0.90	3	-
GCF_018119395.1	s__Massilia sp018119395	81.9299	948	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_003011895.2	s__Massilia glaciei	81.7642	885	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461825.1	s__Rugamonas sp016461825	81.4453	899	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614195.1	s__Massilia horti	81.4422	817	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:34,347] [INFO] GTDB search result was written to GCF_016809835.1_ASM1680983v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:34,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:34,350] [INFO] DFAST_QC result json was written to GCF_016809835.1_ASM1680983v2_genomic.fna/dqc_result.json
[2024-01-24 14:32:34,351] [INFO] DFAST_QC completed!
[2024-01-24 14:32:34,351] [INFO] Total running time: 0h1m49s