[2024-01-24 10:47:06,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference
[2024-01-24 10:47:12,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg66f691b2-ffba-4d06-96eb-264ef827158f/GCF_020831365.1_ASM2083136v1_genomic.fna.gz | prodigal -d GCF_020831365.1_ASM2083136v1_genomic.fna/cds.fna -a GCF_020831365.1_ASM2083136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:26,473] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:26,473] [INFO] Task started: HMMsearch
[2024-01-24 10:47:26,473] [INFO] Running command: hmmsearch --tblout GCF_020831365.1_ASM2083136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference/reference_markers.hmm GCF_020831365.1_ASM2083136v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:26,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:26,788] [INFO] Found 6/6 markers.
[2024-01-24 10:47:26,831] [INFO] Query marker FASTA was written to GCF_020831365.1_ASM2083136v1_genomic.fna/markers.fasta
[2024-01-24 10:47:26,832] [INFO] Task started: Blastn
[2024-01-24 10:47:26,832] [INFO] Running command: blastn -query GCF_020831365.1_ASM2083136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference/reference_markers.fasta -out GCF_020831365.1_ASM2083136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:27,857] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:27,862] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:27,863] [INFO] Target genome list was writen to GCF_020831365.1_ASM2083136v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:27,871] [INFO] Task started: fastANI
[2024-01-24 10:47:27,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f691b2-ffba-4d06-96eb-264ef827158f/GCF_020831365.1_ASM2083136v1_genomic.fna.gz --refList GCF_020831365.1_ASM2083136v1_genomic.fna/target_genomes.txt --output GCF_020831365.1_ASM2083136v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:47,017] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:47,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:47,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:47,033] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:47,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:47,034] [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 polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	89.1333	1191	1547	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	88.018	1298	1547	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	85.5715	1025	1547	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.7465	1005	1547	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	82.3454	1000	1547	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	82.2984	976	1547	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	82.202	996	1547	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	82.1909	976	1547	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.5061	909	1547	95	below_threshold
Massilia arenae	strain=GEM5	GCA_008014745.1	2603288	2603288	type	True	81.3928	885	1547	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	81.34	908	1547	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.3192	872	1547	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	80.4686	830	1547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:47,046] [INFO] DFAST Taxonomy check result was written to GCF_020831365.1_ASM2083136v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:47,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:47,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:47,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference/checkm_data
[2024-01-24 10:47:47,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:47,117] [INFO] Task started: CheckM
[2024-01-24 10:47:47,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020831365.1_ASM2083136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020831365.1_ASM2083136v1_genomic.fna/checkm_input GCF_020831365.1_ASM2083136v1_genomic.fna/checkm_result
[2024-01-24 10:48:29,469] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:29,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,486] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:29,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:29,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020831365.1_ASM2083136v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:29,487] [INFO] Task started: Blastn
[2024-01-24 10:48:29,487] [INFO] Running command: blastn -query GCF_020831365.1_ASM2083136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28cdf927-86e9-4b0f-b29a-4a386d3afb5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020831365.1_ASM2083136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:31,367] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:31,370] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:31,370] [INFO] Target genome list was writen to GCF_020831365.1_ASM2083136v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:31,387] [INFO] Task started: fastANI
[2024-01-24 10:48:31,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f691b2-ffba-4d06-96eb-264ef827158f/GCF_020831365.1_ASM2083136v1_genomic.fna.gz --refList GCF_020831365.1_ASM2083136v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020831365.1_ASM2083136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:51,817] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:51,830] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:51,830] [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	89.1244	1192	1547	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	85.5395	1028	1547	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	82.753	1005	1547	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	82.3502	1000	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	82.327	865	1547	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	82.2973	977	1547	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	82.2853	994	1547	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	82.2167	972	1547	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	82.2045	995	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_000382345.1	s__Massilia niastensis	82.1904	936	1547	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	82.0591	929	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCA_002354135.1	s__Massilia sp002354135	82.0322	762	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506415.1	s__Massilia sp902506415	81.6934	952	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011895.2	s__Massilia glaciei	81.5114	859	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849555.1	s__Massilia sp012849555	81.2967	915	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129765.1	s__Massilia sp900129765	81.0237	827	1547	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 10:48:51,832] [INFO] GTDB search result was written to GCF_020831365.1_ASM2083136v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:51,833] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:51,836] [INFO] DFAST_QC result json was written to GCF_020831365.1_ASM2083136v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:51,837] [INFO] DFAST_QC completed!
[2024-01-24 10:48:51,837] [INFO] Total running time: 0h1m45s