[2024-01-25 20:18:35,607] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:35,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:35,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference
[2024-01-25 20:18:36,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:36,714] [INFO] Task started: Prodigal
[2024-01-25 20:18:36,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg4892ad73-8d5e-4bd2-90b2-6fedc2997436/GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/cds.fna -a GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:44,527] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:44,528] [INFO] Task started: HMMsearch
[2024-01-25 20:18:44,528] [INFO] Running command: hmmsearch --tblout GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference/reference_markers.hmm GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:44,748] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:44,750] [INFO] Found 6/6 markers.
[2024-01-25 20:18:44,773] [INFO] Query marker FASTA was written to GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:18:44,773] [INFO] Task started: Blastn
[2024-01-25 20:18:44,773] [INFO] Running command: blastn -query GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference/reference_markers.fasta -out GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:45,674] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:45,678] [INFO] Selected 17 target genomes.
[2024-01-25 20:18:45,678] [INFO] Target genome list was writen to GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:18:45,695] [INFO] Task started: fastANI
[2024-01-25 20:18:45,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg4892ad73-8d5e-4bd2-90b2-6fedc2997436/GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna.gz --refList GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:58,109] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:58,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:58,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:58,121] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:58,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:58,121] [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
Propionibacterium cyclohexanicum	strain=DSM 16859	GCA_900111365.1	64702	64702	type	True	100.0	906	907	95	conclusive
Propionibacterium acidifaciens	strain=DSM 21887	GCA_000426605.1	556499	556499	type	True	78.8961	319	907	95	below_threshold
Propionibacterium freudenreichii subsp. freudenreichii	strain=DSM 20271	GCA_000940845.1	66712	1744	type	True	78.5458	336	907	95	below_threshold
Propionibacterium australiense	strain=NCTC13651	GCA_900637915.1	119981	119981	type	True	78.4783	299	907	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	78.4596	298	907	95	below_threshold
Acidipropionibacterium jensenii	strain=DSM 20535	GCA_000425285.1	1749	1749	type	True	77.2394	195	907	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	76.8777	190	907	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	76.6638	174	907	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	76.6489	146	907	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	76.5353	163	907	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	76.2873	118	907	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	75.9857	146	907	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	75.9059	110	907	95	below_threshold
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	75.6226	92	907	95	below_threshold
Streptomyces coryli	strain=A7024	GCA_011044975.1	1128680	1128680	type	True	75.5246	135	907	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.5051	152	907	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	75.419	113	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:58,123] [INFO] DFAST Taxonomy check result was written to GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:18:58,123] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:58,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:58,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference/checkm_data
[2024-01-25 20:18:58,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:58,153] [INFO] Task started: CheckM
[2024-01-25 20:18:58,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/checkm_input GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:19:34,407] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:34,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:34,427] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:34,428] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:34,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:19:34,428] [INFO] Task started: Blastn
[2024-01-25 20:19:34,428] [INFO] Running command: blastn -query GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2850a6e7-9a17-4a5d-a03d-248d5d5af94f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:35,904] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:35,907] [INFO] Selected 13 target genomes.
[2024-01-25 20:19:35,907] [INFO] Target genome list was writen to GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:35,943] [INFO] Task started: fastANI
[2024-01-25 20:19:35,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg4892ad73-8d5e-4bd2-90b2-6fedc2997436/GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna.gz --refList GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:44,151] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:44,159] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:44,160] [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_900111365.1	s__Propionibacterium cyclohexanicum	100.0	906	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426605.1	s__Propionibacterium acidifaciens	78.8439	323	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.24	99.02	0.93	0.90	4	-
GCF_900289195.1	s__Propionibacterium sp900289195	78.5571	270	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.03	99.03	0.94	0.94	2	-
GCF_000940845.1	s__Propionibacterium freudenreichii	78.5442	336	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	98.89	98.71	0.93	0.90	43	-
GCF_003666605.1	s__Propionibacterium australiense	78.4676	298	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.91	99.75	0.98	0.97	4	-
GCF_000425285.1	s__Acidipropionibacterium jensenii	77.2541	194	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	98.58	97.66	0.92	0.89	5	-
GCF_001693815.1	s__Arachnia lapidicapta	76.6489	146	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.86	97.76	0.95	0.93	4	-
GCF_003344635.1	s__Desertihabitans aurantiacus	76.5228	164	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCA_012517965.1	s__Propioniciclava sp012517965	76.4089	133	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837465.1	s__Arachnia sp012837465	76.3971	119	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	76.0959	142	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000426525.1	s__Nocardioides alkalitolerans	75.7987	133	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340985.1	s__Nocardiopsis valliformis	75.6124	93	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:44,161] [INFO] GTDB search result was written to GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:44,161] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:44,165] [INFO] DFAST_QC result json was written to GCF_900111365.1_IMG-taxon_2675903216_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:19:44,165] [INFO] DFAST_QC completed!
[2024-01-25 20:19:44,165] [INFO] Total running time: 0h1m9s