[2024-01-24 14:30:16,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference
[2024-01-24 14:30:17,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:17,847] [INFO] Task started: Prodigal
[2024-01-24 14:30:17,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg3680b478-0d43-4a30-9741-89e3afff9571/GCF_013377855.1_ASM1337785v1_genomic.fna.gz | prodigal -d GCF_013377855.1_ASM1337785v1_genomic.fna/cds.fna -a GCF_013377855.1_ASM1337785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:29,424] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:29,425] [INFO] Task started: HMMsearch
[2024-01-24 14:30:29,425] [INFO] Running command: hmmsearch --tblout GCF_013377855.1_ASM1337785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference/reference_markers.hmm GCF_013377855.1_ASM1337785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:29,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:29,718] [INFO] Found 6/6 markers.
[2024-01-24 14:30:29,751] [INFO] Query marker FASTA was written to GCF_013377855.1_ASM1337785v1_genomic.fna/markers.fasta
[2024-01-24 14:30:29,751] [INFO] Task started: Blastn
[2024-01-24 14:30:29,751] [INFO] Running command: blastn -query GCF_013377855.1_ASM1337785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference/reference_markers.fasta -out GCF_013377855.1_ASM1337785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:30,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:30,506] [INFO] Selected 15 target genomes.
[2024-01-24 14:30:30,507] [INFO] Target genome list was writen to GCF_013377855.1_ASM1337785v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:30,576] [INFO] Task started: fastANI
[2024-01-24 14:30:30,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg3680b478-0d43-4a30-9741-89e3afff9571/GCF_013377855.1_ASM1337785v1_genomic.fna.gz --refList GCF_013377855.1_ASM1337785v1_genomic.fna/target_genomes.txt --output GCF_013377855.1_ASM1337785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:44,010] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:44,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:44,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:44,023] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:44,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:44,023] [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
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	100.0	1207	1208	95	conclusive
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	92.511	1059	1208	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	79.2482	456	1208	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	79.2456	451	1208	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	79.1302	446	1208	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.7576	332	1208	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.4295	412	1208	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	78.3549	369	1208	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	77.2761	151	1208	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	76.8579	130	1208	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.7144	157	1208	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.466	139	1208	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	76.0568	108	1208	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	75.6949	52	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:44,025] [INFO] DFAST Taxonomy check result was written to GCF_013377855.1_ASM1337785v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:44,025] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:44,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:44,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference/checkm_data
[2024-01-24 14:30:44,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:44,071] [INFO] Task started: CheckM
[2024-01-24 14:30:44,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377855.1_ASM1337785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377855.1_ASM1337785v1_genomic.fna/checkm_input GCF_013377855.1_ASM1337785v1_genomic.fna/checkm_result
[2024-01-24 14:31:22,047] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:22,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:22,075] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:22,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:22,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377855.1_ASM1337785v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:22,077] [INFO] Task started: Blastn
[2024-01-24 14:31:22,077] [INFO] Running command: blastn -query GCF_013377855.1_ASM1337785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f13381b-f9f7-4134-a150-c20bbd5b7b65/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377855.1_ASM1337785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:23,331] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:23,335] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:23,335] [INFO] Target genome list was writen to GCF_013377855.1_ASM1337785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:23,342] [INFO] Task started: fastANI
[2024-01-24 14:31:23,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg3680b478-0d43-4a30-9741-89e3afff9571/GCF_013377855.1_ASM1337785v1_genomic.fna.gz --refList GCF_013377855.1_ASM1337785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377855.1_ASM1337785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:32,593] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:32,603] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:32,603] [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_013377855.1	s__Undibacterium oligocarboniphilum	100.0	1207	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014284195.1	s__Undibacterium sp014284195	92.511	1059	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284235.1	s__Undibacterium sp014284235	79.2621	450	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010078235.1	s__Undibacterium crateris	79.2584	454	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284365.1	s__Undibacterium sp014284365	79.1461	444	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014284255.1	s__Undibacterium jejuense	78.7448	333	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284335.1	s__Undibacterium sp014284335	78.4603	410	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201815.1	s__Undibacterium pigrum	78.3629	367	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927585.1	s__AVCC01 sp012927585	76.5637	132	1208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614185.1	s__Massilia arenosa	76.0717	107	1208	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 14:31:32,605] [INFO] GTDB search result was written to GCF_013377855.1_ASM1337785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:32,605] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:32,608] [INFO] DFAST_QC result json was written to GCF_013377855.1_ASM1337785v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:32,609] [INFO] DFAST_QC completed!
[2024-01-24 14:31:32,609] [INFO] Total running time: 0h1m16s