[2024-01-24 13:55:14,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference
[2024-01-24 13:55:15,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:15,722] [INFO] Task started: Prodigal
[2024-01-24 13:55:15,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg70225e0e-d637-40df-9eb9-8a707c02b8e3/GCF_013778455.1_ASM1377845v1_genomic.fna.gz | prodigal -d GCF_013778455.1_ASM1377845v1_genomic.fna/cds.fna -a GCF_013778455.1_ASM1377845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:42,793] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:42,794] [INFO] Task started: HMMsearch
[2024-01-24 13:55:42,794] [INFO] Running command: hmmsearch --tblout GCF_013778455.1_ASM1377845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference/reference_markers.hmm GCF_013778455.1_ASM1377845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:43,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:43,200] [INFO] Found 6/6 markers.
[2024-01-24 13:55:43,274] [INFO] Query marker FASTA was written to GCF_013778455.1_ASM1377845v1_genomic.fna/markers.fasta
[2024-01-24 13:55:43,275] [INFO] Task started: Blastn
[2024-01-24 13:55:43,275] [INFO] Running command: blastn -query GCF_013778455.1_ASM1377845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference/reference_markers.fasta -out GCF_013778455.1_ASM1377845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:44,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:44,684] [INFO] Selected 20 target genomes.
[2024-01-24 13:55:44,684] [INFO] Target genome list was writen to GCF_013778455.1_ASM1377845v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:44,707] [INFO] Task started: fastANI
[2024-01-24 13:55:44,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg70225e0e-d637-40df-9eb9-8a707c02b8e3/GCF_013778455.1_ASM1377845v1_genomic.fna.gz --refList GCF_013778455.1_ASM1377845v1_genomic.fna/target_genomes.txt --output GCF_013778455.1_ASM1377845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:30,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:30,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:30,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:30,255] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:30,255] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:30,255] [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 himalayensis subsp. himalayensis	strain=PSKA28	GCA_013778455.1	2756131	2820085	type	True	100.0	3036	3040	95	conclusive
Streptomyces himalayensis subsp. aureolus	strain=PSKA54	GCA_013912435.1	2758039	2820085	type	True	97.5247	2522	3040	95	conclusive
Streptomyces jeddahensis	strain=G25	GCA_001642995.1	1716141	1716141	type	True	90.8389	2052	3040	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	83.6185	1696	3040	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	83.3391	1725	3040	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	83.3079	1473	3040	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	83.2878	1640	3040	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	83.2416	1515	3040	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.1558	1832	3040	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	83.0204	1758	3040	95	below_threshold
Streptomyces acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	82.7831	1545	3040	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.7635	1708	3040	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	82.7343	1679	3040	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	82.7201	1508	3040	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	82.6157	1564	3040	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	82.5843	1427	3040	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	82.4555	1509	3040	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	82.3327	1469	3040	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	82.215	1528	3040	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	82.0852	1671	3040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:30,257] [INFO] DFAST Taxonomy check result was written to GCF_013778455.1_ASM1377845v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:30,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:30,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:30,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference/checkm_data
[2024-01-24 13:56:30,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:30,346] [INFO] Task started: CheckM
[2024-01-24 13:56:30,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013778455.1_ASM1377845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013778455.1_ASM1377845v1_genomic.fna/checkm_input GCF_013778455.1_ASM1377845v1_genomic.fna/checkm_result
[2024-01-24 13:57:58,620] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:58,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:58,671] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:58,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:58,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013778455.1_ASM1377845v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:58,672] [INFO] Task started: Blastn
[2024-01-24 13:57:58,672] [INFO] Running command: blastn -query GCF_013778455.1_ASM1377845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb33c2abb-01b7-49e1-90b4-a47eda154541/dqc_reference/reference_markers_gtdb.fasta -out GCF_013778455.1_ASM1377845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,896] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,900] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:00,900] [INFO] Target genome list was writen to GCF_013778455.1_ASM1377845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:00,915] [INFO] Task started: fastANI
[2024-01-24 13:58:00,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg70225e0e-d637-40df-9eb9-8a707c02b8e3/GCF_013778455.1_ASM1377845v1_genomic.fna.gz --refList GCF_013778455.1_ASM1377845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013778455.1_ASM1377845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:58,006] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:58,027] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:58,027] [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_013778455.1	s__Streptomyces himalayensis	100.0	3036	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.53	97.53	0.86	0.86	2	conclusive
GCF_001642995.1	s__Streptomyces jeddahensis	90.8349	2051	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	83.5995	1700	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	83.5841	1807	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300165.1	s__Streptomyces sp002300165	83.4013	1553	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.35	96.35	0.87	0.87	2	-
GCF_007050945.1	s__Streptomyces sp007050945	83.3798	1787	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377205.1	s__Streptomyces phyllanthi	83.3209	1471	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645835.1	s__Streptomyces albiflavescens	83.315	1730	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	83.258	1511	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_016598615.1	s__Streptomyces sp016598615	83.2454	1765	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	83.2035	1652	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_003664315.1	s__Streptomyces sp003664315	83.201	1560	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	83.0848	1715	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000719105.1	s__Streptomyces sclerotialus_B	83.0765	1451	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514115.1	s__Streptomyces olivochromogenes	83.0389	1754	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_002920535.1	s__Streptomyces sp002920535	82.8137	1512	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	82.763	1675	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	82.6658	1589	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	82.6234	1562	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	82.5384	1408	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	82.5065	1515	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755605.1	s__Streptomyces typhae	82.2689	1453	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
GCF_002217755.1	s__Streptomyces hyaluromycini	82.0751	1672	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.22	96.22	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:58,029] [INFO] GTDB search result was written to GCF_013778455.1_ASM1377845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:58,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:58,035] [INFO] DFAST_QC result json was written to GCF_013778455.1_ASM1377845v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:58,035] [INFO] DFAST_QC completed!
[2024-01-24 13:58:58,035] [INFO] Total running time: 0h3m44s