[2024-01-24 13:27:25,426] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:25,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:25,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference
[2024-01-24 13:27:26,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:26,602] [INFO] Task started: Prodigal
[2024-01-24 13:27:26,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg25227731-dc72-4bd7-8045-dfd50030e68b/GCF_014284195.1_ASM1428419v1_genomic.fna.gz | prodigal -d GCF_014284195.1_ASM1428419v1_genomic.fna/cds.fna -a GCF_014284195.1_ASM1428419v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:37,227] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:37,227] [INFO] Task started: HMMsearch
[2024-01-24 13:27:37,228] [INFO] Running command: hmmsearch --tblout GCF_014284195.1_ASM1428419v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference/reference_markers.hmm GCF_014284195.1_ASM1428419v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:37,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:37,493] [INFO] Found 6/6 markers.
[2024-01-24 13:27:37,525] [INFO] Query marker FASTA was written to GCF_014284195.1_ASM1428419v1_genomic.fna/markers.fasta
[2024-01-24 13:27:37,525] [INFO] Task started: Blastn
[2024-01-24 13:27:37,525] [INFO] Running command: blastn -query GCF_014284195.1_ASM1428419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference/reference_markers.fasta -out GCF_014284195.1_ASM1428419v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:38,235] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:38,238] [INFO] Selected 15 target genomes.
[2024-01-24 13:27:38,239] [INFO] Target genome list was writen to GCF_014284195.1_ASM1428419v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:38,292] [INFO] Task started: fastANI
[2024-01-24 13:27:38,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg25227731-dc72-4bd7-8045-dfd50030e68b/GCF_014284195.1_ASM1428419v1_genomic.fna.gz --refList GCF_014284195.1_ASM1428419v1_genomic.fna/target_genomes.txt --output GCF_014284195.1_ASM1428419v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:50,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:50,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:50,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:50,738] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:50,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:50,739] [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 griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	100.0	1194	1195	95	conclusive
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	92.487	1056	1195	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	79.918	507	1195	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	79.5549	474	1195	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	79.4967	452	1195	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	79.4147	491	1195	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.7694	327	1195	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.5769	441	1195	95	below_threshold
Undibacterium terreum	strain=CGMCC 1.10998	GCA_014636315.1	1224302	1224302	type	True	78.0808	341	1195	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.9813	177	1195	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.947	164	1195	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	76.9267	137	1195	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.8678	138	1195	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.4732	147	1195	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.2768	52	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:50,740] [INFO] DFAST Taxonomy check result was written to GCF_014284195.1_ASM1428419v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:50,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:50,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:50,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference/checkm_data
[2024-01-24 13:27:50,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:50,781] [INFO] Task started: CheckM
[2024-01-24 13:27:50,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284195.1_ASM1428419v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284195.1_ASM1428419v1_genomic.fna/checkm_input GCF_014284195.1_ASM1428419v1_genomic.fna/checkm_result
[2024-01-24 13:28:27,263] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:27,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:27,284] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:27,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:27,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284195.1_ASM1428419v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:27,286] [INFO] Task started: Blastn
[2024-01-24 13:28:27,286] [INFO] Running command: blastn -query GCF_014284195.1_ASM1428419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f4a4cd-dec4-4dd1-a32a-36beddaa62fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284195.1_ASM1428419v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:28,639] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:28,643] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:28,643] [INFO] Target genome list was writen to GCF_014284195.1_ASM1428419v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:28,667] [INFO] Task started: fastANI
[2024-01-24 13:28:28,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg25227731-dc72-4bd7-8045-dfd50030e68b/GCF_014284195.1_ASM1428419v1_genomic.fna.gz --refList GCF_014284195.1_ASM1428419v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284195.1_ASM1428419v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:38,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:38,050] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:38,051] [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_014284195.1	s__Undibacterium sp014284195	100.0	1194	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013377855.1	s__Undibacterium oligocarboniphilum	92.487	1056	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014699135.1	s__Undibacterium aquatile	79.918	507	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
GCF_010078235.1	s__Undibacterium crateris	79.5796	470	1195	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	79.4984	451	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014284235.1	s__Undibacterium sp014284235	79.4049	492	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016196925.1	s__Undibacterium sp016196925	78.9386	409	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284255.1	s__Undibacterium jejuense	78.7568	328	1195	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	78.5809	440	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000026125.1	s__Herminiimonas arsenicoxydans	77.3922	161	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217275.1	s__Pseudoduganella sp004217275	76.5251	165	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:38,052] [INFO] GTDB search result was written to GCF_014284195.1_ASM1428419v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:38,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:38,056] [INFO] DFAST_QC result json was written to GCF_014284195.1_ASM1428419v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:38,056] [INFO] DFAST_QC completed!
[2024-01-24 13:28:38,056] [INFO] Total running time: 0h1m13s