[2024-01-24 14:23:02,296] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:02,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:02,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference
[2024-01-24 14:23:03,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:03,597] [INFO] Task started: Prodigal
[2024-01-24 14:23:03,597] [INFO] Running command: gunzip -c /var/lib/cwl/stge421277f-33a8-488c-8dbc-6fb2ec877ac4/GCF_014205255.1_ASM1420525v1_genomic.fna.gz | prodigal -d GCF_014205255.1_ASM1420525v1_genomic.fna/cds.fna -a GCF_014205255.1_ASM1420525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:30,552] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:30,552] [INFO] Task started: HMMsearch
[2024-01-24 14:23:30,552] [INFO] Running command: hmmsearch --tblout GCF_014205255.1_ASM1420525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference/reference_markers.hmm GCF_014205255.1_ASM1420525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:31,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:31,053] [INFO] Found 6/6 markers.
[2024-01-24 14:23:31,155] [INFO] Query marker FASTA was written to GCF_014205255.1_ASM1420525v1_genomic.fna/markers.fasta
[2024-01-24 14:23:31,156] [INFO] Task started: Blastn
[2024-01-24 14:23:31,156] [INFO] Running command: blastn -query GCF_014205255.1_ASM1420525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference/reference_markers.fasta -out GCF_014205255.1_ASM1420525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:32,494] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:32,496] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:32,497] [INFO] Target genome list was writen to GCF_014205255.1_ASM1420525v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:32,501] [INFO] Task started: fastANI
[2024-01-24 14:23:32,502] [INFO] Running command: fastANI --query /var/lib/cwl/stge421277f-33a8-488c-8dbc-6fb2ec877ac4/GCF_014205255.1_ASM1420525v1_genomic.fna.gz --refList GCF_014205255.1_ASM1420525v1_genomic.fna/target_genomes.txt --output GCF_014205255.1_ASM1420525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:03,752] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:03,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:03,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:03,770] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:24:03,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:24:03,771] [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
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	100.0	2972	2978	95	conclusive
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	99.9852	2919	2978	95	conclusive
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	94.6247	2259	2978	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	94.1347	2050	2978	95	below_threshold
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	94.0023	2305	2978	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	93.9854	2345	2978	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	92.9265	1973	2978	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.5802	2257	2978	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	91.3038	2227	2978	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.246	1846	2978	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	89.8651	2184	2978	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	89.7981	1871	2978	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.4943	1733	2978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:03,772] [INFO] DFAST Taxonomy check result was written to GCF_014205255.1_ASM1420525v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:03,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:03,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:03,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference/checkm_data
[2024-01-24 14:24:03,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:03,853] [INFO] Task started: CheckM
[2024-01-24 14:24:03,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205255.1_ASM1420525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205255.1_ASM1420525v1_genomic.fna/checkm_input GCF_014205255.1_ASM1420525v1_genomic.fna/checkm_result
[2024-01-24 14:26:23,131] [INFO] Task succeeded: CheckM
[2024-01-24 14:26:23,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:26:23,157] [INFO] ===== Completeness check finished =====
[2024-01-24 14:26:23,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:26:23,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205255.1_ASM1420525v1_genomic.fna/markers.fasta)
[2024-01-24 14:26:23,158] [INFO] Task started: Blastn
[2024-01-24 14:26:23,158] [INFO] Running command: blastn -query GCF_014205255.1_ASM1420525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a196981-ec6c-4a8f-8199-be2d6ac1c003/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205255.1_ASM1420525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:26:25,294] [INFO] Task succeeded: Blastn
[2024-01-24 14:26:25,301] [INFO] Selected 8 target genomes.
[2024-01-24 14:26:25,302] [INFO] Target genome list was writen to GCF_014205255.1_ASM1420525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:26:25,322] [INFO] Task started: fastANI
[2024-01-24 14:26:25,323] [INFO] Running command: fastANI --query /var/lib/cwl/stge421277f-33a8-488c-8dbc-6fb2ec877ac4/GCF_014205255.1_ASM1420525v1_genomic.fna.gz --refList GCF_014205255.1_ASM1420525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205255.1_ASM1420525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:45,560] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:45,573] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:45,574] [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_014205255.1	s__Streptomyces caelestis	100.0	2974	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002148965.1	s__Streptomyces swartbergensis	94.165	2046	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	94.0088	2344	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCA_000415505.1	s__Streptomyces afghaniensis	93.4837	2156	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	93.4551	2302	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002150735.1	s__Streptomyces africanus	92.9587	1969	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611795.1	s__Streptomyces qaidamensis	90.39	2255	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_007655005.1	s__Streptomyces tibetensis	89.8775	2182	2978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:45,575] [INFO] GTDB search result was written to GCF_014205255.1_ASM1420525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:45,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:45,579] [INFO] DFAST_QC result json was written to GCF_014205255.1_ASM1420525v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:45,580] [INFO] DFAST_QC completed!
[2024-01-24 14:26:45,580] [INFO] Total running time: 0h3m43s