[2024-01-24 13:12:38,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference
[2024-01-24 13:12:40,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,296] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,296] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb380ddf-86de-4de2-9f9f-42deef1304b9/GCF_006094415.1_ASM609441v1_genomic.fna.gz | prodigal -d GCF_006094415.1_ASM609441v1_genomic.fna/cds.fna -a GCF_006094415.1_ASM609441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:48,107] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:48,108] [INFO] Task started: HMMsearch
[2024-01-24 13:12:48,108] [INFO] Running command: hmmsearch --tblout GCF_006094415.1_ASM609441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference/reference_markers.hmm GCF_006094415.1_ASM609441v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:48,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:48,386] [INFO] Found 6/6 markers.
[2024-01-24 13:12:48,416] [INFO] Query marker FASTA was written to GCF_006094415.1_ASM609441v1_genomic.fna/markers.fasta
[2024-01-24 13:12:48,417] [INFO] Task started: Blastn
[2024-01-24 13:12:48,417] [INFO] Running command: blastn -query GCF_006094415.1_ASM609441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference/reference_markers.fasta -out GCF_006094415.1_ASM609441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:49,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:49,733] [INFO] Selected 9 target genomes.
[2024-01-24 13:12:49,734] [INFO] Target genome list was writen to GCF_006094415.1_ASM609441v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:49,738] [INFO] Task started: fastANI
[2024-01-24 13:12:49,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb380ddf-86de-4de2-9f9f-42deef1304b9/GCF_006094415.1_ASM609441v1_genomic.fna.gz --refList GCF_006094415.1_ASM609441v1_genomic.fna/target_genomes.txt --output GCF_006094415.1_ASM609441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:56,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:56,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:56,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:56,671] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:12:56,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:56,672] [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
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	99.9514	805	853	95	conclusive
Micrococcus luteus	strain=NCTC 2665	GCA_000023205.1	1270	1270	type	True	99.9272	806	853	95	conclusive
Micrococcus luteus	strain=ATCC 4698	GCA_008868275.1	1270	1270	type	True	99.7199	661	853	95	conclusive
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	99.5823	581	853	95	conclusive
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	89.1003	696	853	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	84.3753	617	853	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.0596	261	853	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.0214	238	853	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.7769	276	853	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:56,680] [INFO] DFAST Taxonomy check result was written to GCF_006094415.1_ASM609441v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:56,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:56,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:56,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference/checkm_data
[2024-01-24 13:12:56,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:56,724] [INFO] Task started: CheckM
[2024-01-24 13:12:56,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006094415.1_ASM609441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006094415.1_ASM609441v1_genomic.fna/checkm_input GCF_006094415.1_ASM609441v1_genomic.fna/checkm_result
[2024-01-24 13:13:48,188] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:48,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:48,210] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:48,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:48,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006094415.1_ASM609441v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:48,211] [INFO] Task started: Blastn
[2024-01-24 13:13:48,212] [INFO] Running command: blastn -query GCF_006094415.1_ASM609441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6704d098-7552-4fae-b7dc-ac1076869901/dqc_reference/reference_markers_gtdb.fasta -out GCF_006094415.1_ASM609441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:50,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:50,180] [INFO] Selected 6 target genomes.
[2024-01-24 13:13:50,180] [INFO] Target genome list was writen to GCF_006094415.1_ASM609441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:50,186] [INFO] Task started: fastANI
[2024-01-24 13:13:50,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb380ddf-86de-4de2-9f9f-42deef1304b9/GCF_006094415.1_ASM609441v1_genomic.fna.gz --refList GCF_006094415.1_ASM609441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006094415.1_ASM609441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:54,338] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:54,349] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:54,350] [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_000023205.1	s__Micrococcus luteus	99.9272	806	853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	conclusive
GCF_014205115.1	s__Micrococcus endophyticus	89.1212	695	853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_014204815.1	s__Micrococcus flavus	84.4332	632	853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001570885.1	s__Micrococcus lylae	82.8928	552	853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	-
GCF_014205175.1	s__Micrococcus cohnii	81.1102	474	853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.00	98.97	0.96	0.96	3	-
GCF_005877055.1	s__Citricoccus sp005877055	80.6255	494	853	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:54,352] [INFO] GTDB search result was written to GCF_006094415.1_ASM609441v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:54,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:54,355] [INFO] DFAST_QC result json was written to GCF_006094415.1_ASM609441v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:54,355] [INFO] DFAST_QC completed!
[2024-01-24 13:13:54,356] [INFO] Total running time: 0h1m15s