[2024-01-24 14:46:57,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference
[2024-01-24 14:46:58,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,353] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e486642-6b9d-4279-9b2c-fb68982f212e/GCF_013433285.1_ASM1343328v1_genomic.fna.gz | prodigal -d GCF_013433285.1_ASM1343328v1_genomic.fna/cds.fna -a GCF_013433285.1_ASM1343328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:25,909] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:25,909] [INFO] Task started: HMMsearch
[2024-01-24 14:47:25,909] [INFO] Running command: hmmsearch --tblout GCF_013433285.1_ASM1343328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference/reference_markers.hmm GCF_013433285.1_ASM1343328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:26,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:26,318] [INFO] Found 6/6 markers.
[2024-01-24 14:47:26,400] [INFO] Query marker FASTA was written to GCF_013433285.1_ASM1343328v1_genomic.fna/markers.fasta
[2024-01-24 14:47:26,400] [INFO] Task started: Blastn
[2024-01-24 14:47:26,400] [INFO] Running command: blastn -query GCF_013433285.1_ASM1343328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference/reference_markers.fasta -out GCF_013433285.1_ASM1343328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:27,814] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:27,818] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:27,818] [INFO] Target genome list was writen to GCF_013433285.1_ASM1343328v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:27,822] [INFO] Task started: fastANI
[2024-01-24 14:47:27,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e486642-6b9d-4279-9b2c-fb68982f212e/GCF_013433285.1_ASM1343328v1_genomic.fna.gz --refList GCF_013433285.1_ASM1343328v1_genomic.fna/target_genomes.txt --output GCF_013433285.1_ASM1343328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:00,111] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:00,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:00,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:00,128] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:48:00,128] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:48:00,129] [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 gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	100.0	3037	3045	95	inconclusive
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	95.2205	2357	3045	95	inconclusive
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	95.2018	2403	3045	95	inconclusive
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	91.176	1890	3045	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	90.9549	1915	3045	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.0696	1914	3045	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.7568	1756	3045	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.466	1949	3045	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.3952	1669	3045	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2209	1472	3045	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	84.831	1772	3045	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	84.6718	1807	3045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:00,135] [INFO] DFAST Taxonomy check result was written to GCF_013433285.1_ASM1343328v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:00,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:00,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:00,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference/checkm_data
[2024-01-24 14:48:00,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:00,233] [INFO] Task started: CheckM
[2024-01-24 14:48:00,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013433285.1_ASM1343328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013433285.1_ASM1343328v1_genomic.fna/checkm_input GCF_013433285.1_ASM1343328v1_genomic.fna/checkm_result
[2024-01-24 14:50:12,043] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:12,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:12,074] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:12,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:12,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013433285.1_ASM1343328v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:12,075] [INFO] Task started: Blastn
[2024-01-24 14:50:12,075] [INFO] Running command: blastn -query GCF_013433285.1_ASM1343328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5731bd4b-280b-409b-ba3b-c75566b5a14a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013433285.1_ASM1343328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:14,275] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:14,279] [INFO] Selected 13 target genomes.
[2024-01-24 14:50:14,279] [INFO] Target genome list was writen to GCF_013433285.1_ASM1343328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:14,288] [INFO] Task started: fastANI
[2024-01-24 14:50:14,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e486642-6b9d-4279-9b2c-fb68982f212e/GCF_013433285.1_ASM1343328v1_genomic.fna.gz --refList GCF_013433285.1_ASM1343328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013433285.1_ASM1343328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:44,466] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:44,484] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:44,484] [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_006539505.1	s__Streptomyces spinoverrucosus	95.2263	2357	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	conclusive
GCF_019219825.1	s__Streptomyces sp019219825	93.756	2208	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	92.5721	2157	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	91.1759	1890	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_004187715.1	s__Streptomyces sp004187715	88.5781	2005	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	86.5587	1859	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	86.1359	1959	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_019049285.1	s__Streptomyces sp019049285	85.8936	1950	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	85.7501	1929	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	84.9373	1728	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046785.1	s__Streptomyces sp013046785	84.9151	1700	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	84.8737	1823	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_002920615.1	s__Streptomyces sp002920615	84.8115	1779	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:44,485] [INFO] GTDB search result was written to GCF_013433285.1_ASM1343328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:44,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:44,490] [INFO] DFAST_QC result json was written to GCF_013433285.1_ASM1343328v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:44,490] [INFO] DFAST_QC completed!
[2024-01-24 14:50:44,490] [INFO] Total running time: 0h3m47s