[2024-01-24 14:30:30,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,991] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference
[2024-01-24 14:30:32,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:32,221] [INFO] Task started: Prodigal
[2024-01-24 14:30:32,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg6815b534-b47c-4dc0-82f5-38ae1dfb26d8/GCF_013912435.1_ASM1391243v1_genomic.fna.gz | prodigal -d GCF_013912435.1_ASM1391243v1_genomic.fna/cds.fna -a GCF_013912435.1_ASM1391243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:58,682] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:58,683] [INFO] Task started: HMMsearch
[2024-01-24 14:30:58,683] [INFO] Running command: hmmsearch --tblout GCF_013912435.1_ASM1391243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference/reference_markers.hmm GCF_013912435.1_ASM1391243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:59,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:59,168] [INFO] Found 6/6 markers.
[2024-01-24 14:30:59,250] [INFO] Query marker FASTA was written to GCF_013912435.1_ASM1391243v1_genomic.fna/markers.fasta
[2024-01-24 14:30:59,250] [INFO] Task started: Blastn
[2024-01-24 14:30:59,250] [INFO] Running command: blastn -query GCF_013912435.1_ASM1391243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference/reference_markers.fasta -out GCF_013912435.1_ASM1391243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:00,629] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:00,635] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:00,636] [INFO] Target genome list was writen to GCF_013912435.1_ASM1391243v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:00,645] [INFO] Task started: fastANI
[2024-01-24 14:31:00,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg6815b534-b47c-4dc0-82f5-38ae1dfb26d8/GCF_013912435.1_ASM1391243v1_genomic.fna.gz --refList GCF_013912435.1_ASM1391243v1_genomic.fna/target_genomes.txt --output GCF_013912435.1_ASM1391243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:46,614] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:46,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:46,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:46,637] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:46,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:46,637] [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. aureolus	strain=PSKA54	GCA_013912435.1	2758039	2820085	type	True	100.0	2919	2932	95	conclusive
Streptomyces himalayensis subsp. himalayensis	strain=PSKA28	GCA_013778455.1	2756131	2820085	type	True	97.4805	2513	2932	95	conclusive
Streptomyces jeddahensis	strain=G25	GCA_001642995.1	1716141	1716141	type	True	90.8258	2052	2932	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	83.5425	1684	2932	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	83.4403	1693	2932	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.2145	1787	2932	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	83.1878	1476	2932	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	83.1788	1606	2932	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	83.1031	1706	2932	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	83.0497	1525	2932	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.0326	1553	2932	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	82.8625	1602	2932	95	below_threshold
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	82.8559	1387	2932	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.7763	1686	2932	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	82.6899	1496	2932	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	82.6784	1397	2932	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	82.6102	1648	2932	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	82.5179	1474	2932	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	82.4971	1439	2932	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	82.3132	1415	2932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:46,639] [INFO] DFAST Taxonomy check result was written to GCF_013912435.1_ASM1391243v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:46,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:46,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:46,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference/checkm_data
[2024-01-24 14:31:46,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:46,726] [INFO] Task started: CheckM
[2024-01-24 14:31:46,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013912435.1_ASM1391243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013912435.1_ASM1391243v1_genomic.fna/checkm_input GCF_013912435.1_ASM1391243v1_genomic.fna/checkm_result
[2024-01-24 14:33:08,593] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:08,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:08,622] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:08,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:08,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013912435.1_ASM1391243v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:08,624] [INFO] Task started: Blastn
[2024-01-24 14:33:08,624] [INFO] Running command: blastn -query GCF_013912435.1_ASM1391243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc14c155-d98f-4cf5-a2fc-5af0352577ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_013912435.1_ASM1391243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:10,705] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:10,708] [INFO] Selected 22 target genomes.
[2024-01-24 14:33:10,708] [INFO] Target genome list was writen to GCF_013912435.1_ASM1391243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:10,724] [INFO] Task started: fastANI
[2024-01-24 14:33:10,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg6815b534-b47c-4dc0-82f5-38ae1dfb26d8/GCF_013912435.1_ASM1391243v1_genomic.fna.gz --refList GCF_013912435.1_ASM1391243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013912435.1_ASM1391243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:58,183] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:58,200] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:58,200] [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	97.4724	2515	2932	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	90.8159	2053	2932	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	83.6725	1750	2932	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	83.4306	1694	2932	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	83.4083	1532	2932	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	83.2493	1739	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	83.2488	1738	2932	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	83.2346	1615	2932	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	83.2239	1507	2932	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	83.2097	1472	2932	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	83.1897	1430	2932	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	83.1076	1704	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	83.018	1532	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_014534645.1	s__Streptomyces sp014534645	83.011	1558	2932	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	82.9244	1710	2932	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	82.7806	1553	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920535.1	s__Streptomyces sp002920535	82.7239	1508	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	82.7048	1394	2932	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	82.6829	1497	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646335.1	s__Streptomyces lasiicapitis	82.5427	1469	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_007896895.1	s__Streptomyces misionensis_A	82.2164	1297	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	82.176	1451	2932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:58,202] [INFO] GTDB search result was written to GCF_013912435.1_ASM1391243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:58,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:58,210] [INFO] DFAST_QC result json was written to GCF_013912435.1_ASM1391243v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:58,210] [INFO] DFAST_QC completed!
[2024-01-24 14:33:58,210] [INFO] Total running time: 0h3m27s