[2024-01-24 12:06:23,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference
[2024-01-24 12:06:24,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:24,934] [INFO] Task started: Prodigal
[2024-01-24 12:06:24,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a68cdb2-6bb3-4d4e-bd20-ebf01392ce63/GCF_011682065.1_ASM1168206v1_genomic.fna.gz | prodigal -d GCF_011682065.1_ASM1168206v1_genomic.fna/cds.fna -a GCF_011682065.1_ASM1168206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:49,770] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:49,770] [INFO] Task started: HMMsearch
[2024-01-24 12:06:49,771] [INFO] Running command: hmmsearch --tblout GCF_011682065.1_ASM1168206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference/reference_markers.hmm GCF_011682065.1_ASM1168206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:50,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:50,092] [INFO] Found 6/6 markers.
[2024-01-24 12:06:50,148] [INFO] Query marker FASTA was written to GCF_011682065.1_ASM1168206v1_genomic.fna/markers.fasta
[2024-01-24 12:06:50,149] [INFO] Task started: Blastn
[2024-01-24 12:06:50,149] [INFO] Running command: blastn -query GCF_011682065.1_ASM1168206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference/reference_markers.fasta -out GCF_011682065.1_ASM1168206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:51,221] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:51,225] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:51,226] [INFO] Target genome list was writen to GCF_011682065.1_ASM1168206v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:51,233] [INFO] Task started: fastANI
[2024-01-24 12:06:51,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a68cdb2-6bb3-4d4e-bd20-ebf01392ce63/GCF_011682065.1_ASM1168206v1_genomic.fna.gz --refList GCF_011682065.1_ASM1168206v1_genomic.fna/target_genomes.txt --output GCF_011682065.1_ASM1168206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:09,740] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:09,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:09,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:09,751] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:09,752] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:09,752] [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 rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	100.0	2473	2475	95	conclusive
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	92.4786	2097	2475	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	90.5721	1964	2475	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	89.4837	1920	2475	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	89.3339	1898	2475	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	82.1059	912	2475	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	82.0361	1009	2475	95	below_threshold
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	81.8894	951	2475	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	80.9766	976	2475	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.429	1000	2475	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.3012	1013	2475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:09,756] [INFO] DFAST Taxonomy check result was written to GCF_011682065.1_ASM1168206v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:09,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:09,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:09,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference/checkm_data
[2024-01-24 12:07:09,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:09,827] [INFO] Task started: CheckM
[2024-01-24 12:07:09,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011682065.1_ASM1168206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011682065.1_ASM1168206v1_genomic.fna/checkm_input GCF_011682065.1_ASM1168206v1_genomic.fna/checkm_result
[2024-01-24 12:08:15,977] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:15,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:15,998] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:15,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:15,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011682065.1_ASM1168206v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:15,999] [INFO] Task started: Blastn
[2024-01-24 12:08:15,999] [INFO] Running command: blastn -query GCF_011682065.1_ASM1168206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa13044f-100c-42aa-a0f8-25c04b41bc26/dqc_reference/reference_markers_gtdb.fasta -out GCF_011682065.1_ASM1168206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:17,900] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:17,904] [INFO] Selected 7 target genomes.
[2024-01-24 12:08:17,904] [INFO] Target genome list was writen to GCF_011682065.1_ASM1168206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:17,909] [INFO] Task started: fastANI
[2024-01-24 12:08:17,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a68cdb2-6bb3-4d4e-bd20-ebf01392ce63/GCF_011682065.1_ASM1168206v1_genomic.fna.gz --refList GCF_011682065.1_ASM1168206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011682065.1_ASM1168206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:32,673] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:32,680] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:32,680] [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_011682065.1	s__Massilia rubra	100.0	2473	2475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	conclusive
GCF_011682145.1	s__Massilia mucilaginosa	92.4481	2101	2475	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	92.0479	2095	2475	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	90.5834	1963	2475	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	89.4991	1918	2475	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	89.3526	1895	2475	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	89.2404	1920	2475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.10	97.10	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:32,682] [INFO] GTDB search result was written to GCF_011682065.1_ASM1168206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:32,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:32,685] [INFO] DFAST_QC result json was written to GCF_011682065.1_ASM1168206v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:32,685] [INFO] DFAST_QC completed!
[2024-01-24 12:08:32,685] [INFO] Total running time: 0h2m9s