[2024-01-25 19:44:20,957] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:20,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:20,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference
[2024-01-25 19:44:22,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:22,180] [INFO] Task started: Prodigal
[2024-01-25 19:44:22,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg43b258ab-0376-4e67-84b2-42a7f096985b/GCF_017114865.1_ASM1711486v1_genomic.fna.gz | prodigal -d GCF_017114865.1_ASM1711486v1_genomic.fna/cds.fna -a GCF_017114865.1_ASM1711486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:36,554] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:36,555] [INFO] Task started: HMMsearch
[2024-01-25 19:44:36,555] [INFO] Running command: hmmsearch --tblout GCF_017114865.1_ASM1711486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference/reference_markers.hmm GCF_017114865.1_ASM1711486v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:36,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:36,898] [INFO] Found 6/6 markers.
[2024-01-25 19:44:36,948] [INFO] Query marker FASTA was written to GCF_017114865.1_ASM1711486v1_genomic.fna/markers.fasta
[2024-01-25 19:44:36,949] [INFO] Task started: Blastn
[2024-01-25 19:44:36,949] [INFO] Running command: blastn -query GCF_017114865.1_ASM1711486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference/reference_markers.fasta -out GCF_017114865.1_ASM1711486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:38,246] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:38,249] [INFO] Selected 16 target genomes.
[2024-01-25 19:44:38,249] [INFO] Target genome list was writen to GCF_017114865.1_ASM1711486v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:38,285] [INFO] Task started: fastANI
[2024-01-25 19:44:38,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b258ab-0376-4e67-84b2-42a7f096985b/GCF_017114865.1_ASM1711486v1_genomic.fna.gz --refList GCF_017114865.1_ASM1711486v1_genomic.fna/target_genomes.txt --output GCF_017114865.1_ASM1711486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:05,235] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:05,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:05,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:05,246] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:45:05,246] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:45:05,247] [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 verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	100.0	1973	1978	95	inconclusive
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	95.1565	1655	1978	95	inconclusive
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	95.0625	1640	1978	95	inconclusive
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	94.9236	1662	1978	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	93.763	1637	1978	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	87.4348	1463	1978	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	87.2169	1383	1978	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	86.5661	1405	1978	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	81.2865	946	1978	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	81.1212	986	1978	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.0452	1045	1978	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.9574	1131	1978	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.7877	1014	1978	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	80.7358	1030	1978	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.4899	1035	1978	95	below_threshold
Streptomyces xiaopingdaonensis	strain=DUT 180	GCA_000262345.1	1565415	1565415	type	True	79.9764	815	1978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:05,248] [INFO] DFAST Taxonomy check result was written to GCF_017114865.1_ASM1711486v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:05,248] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:05,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:05,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference/checkm_data
[2024-01-25 19:45:05,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:05,308] [INFO] Task started: CheckM
[2024-01-25 19:45:05,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017114865.1_ASM1711486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017114865.1_ASM1711486v1_genomic.fna/checkm_input GCF_017114865.1_ASM1711486v1_genomic.fna/checkm_result
[2024-01-25 19:46:22,184] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:22,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.60%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:22,205] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:22,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:22,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017114865.1_ASM1711486v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:22,207] [INFO] Task started: Blastn
[2024-01-25 19:46:22,207] [INFO] Running command: blastn -query GCF_017114865.1_ASM1711486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21ceb823-83a9-4913-b96d-8928972117f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017114865.1_ASM1711486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:24,350] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:24,356] [INFO] Selected 10 target genomes.
[2024-01-25 19:46:24,356] [INFO] Target genome list was writen to GCF_017114865.1_ASM1711486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:24,368] [INFO] Task started: fastANI
[2024-01-25 19:46:24,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b258ab-0376-4e67-84b2-42a7f096985b/GCF_017114865.1_ASM1711486v1_genomic.fna.gz --refList GCF_017114865.1_ASM1711486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017114865.1_ASM1711486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:40,869] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:40,876] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:40,876] [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_017114865.1	s__Streptomyces verrucosisporus	100.0	1973	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	conclusive
GCF_002843305.1	s__Streptomyces barkulensis	95.1526	1656	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_900114215.1	s__Streptomyces pini	94.899	1664	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_900110735.1	s__Streptomyces radiopugnans	93.7396	1639	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	87.4589	1459	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	87.2304	1382	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	86.5907	1402	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	81.0525	1048	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	80.7699	999	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262345.1	s__Streptomyces xiaopingdaonensis	79.9947	812	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1625	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:40,878] [INFO] GTDB search result was written to GCF_017114865.1_ASM1711486v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:40,878] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:40,883] [INFO] DFAST_QC result json was written to GCF_017114865.1_ASM1711486v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:40,883] [INFO] DFAST_QC completed!
[2024-01-25 19:46:40,883] [INFO] Total running time: 0h2m20s