[2024-01-24 12:37:08,159] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:08,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:08,161] [INFO] DQC Reference Directory: /var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference
[2024-01-24 12:37:09,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:09,476] [INFO] Task started: Prodigal
[2024-01-24 12:37:09,476] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f9a0b0-6ff3-4b3b-87a2-dc829c2e5ef2/GCF_028863365.1_ASM2886336v1_genomic.fna.gz | prodigal -d GCF_028863365.1_ASM2886336v1_genomic.fna/cds.fna -a GCF_028863365.1_ASM2886336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:37,824] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:37,824] [INFO] Task started: HMMsearch
[2024-01-24 12:37:37,824] [INFO] Running command: hmmsearch --tblout GCF_028863365.1_ASM2886336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference/reference_markers.hmm GCF_028863365.1_ASM2886336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:38,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:38,222] [INFO] Found 6/6 markers.
[2024-01-24 12:37:38,300] [INFO] Query marker FASTA was written to GCF_028863365.1_ASM2886336v1_genomic.fna/markers.fasta
[2024-01-24 12:37:38,301] [INFO] Task started: Blastn
[2024-01-24 12:37:38,301] [INFO] Running command: blastn -query GCF_028863365.1_ASM2886336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference/reference_markers.fasta -out GCF_028863365.1_ASM2886336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:39,657] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:39,660] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:39,661] [INFO] Target genome list was writen to GCF_028863365.1_ASM2886336v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:39,676] [INFO] Task started: fastANI
[2024-01-24 12:37:39,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f9a0b0-6ff3-4b3b-87a2-dc829c2e5ef2/GCF_028863365.1_ASM2886336v1_genomic.fna.gz --refList GCF_028863365.1_ASM2886336v1_genomic.fna/target_genomes.txt --output GCF_028863365.1_ASM2886336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:15,122] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:15,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:15,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:15,142] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:38:15,142] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:38:15,142] [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 neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	99.9718	3184	3271	95	inconclusive
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	99.5801	2249	3271	95	inconclusive
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	95.3868	2140	3271	95	inconclusive
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	94.7576	2092	3271	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	87.7723	2319	3271	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	87.6543	2366	3271	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	87.6127	2312	3271	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	87.5748	2180	3271	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	87.4426	2188	3271	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	87.4284	2320	3271	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.1628	1974	3271	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	83.9177	1940	3271	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	83.713	1763	3271	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	83.2978	1722	3271	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:15,144] [INFO] DFAST Taxonomy check result was written to GCF_028863365.1_ASM2886336v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:15,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:15,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:15,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference/checkm_data
[2024-01-24 12:38:15,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:15,236] [INFO] Task started: CheckM
[2024-01-24 12:38:15,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028863365.1_ASM2886336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028863365.1_ASM2886336v1_genomic.fna/checkm_input GCF_028863365.1_ASM2886336v1_genomic.fna/checkm_result
[2024-01-24 12:40:38,574] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:38,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:38,598] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:38,599] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:38,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028863365.1_ASM2886336v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:38,600] [INFO] Task started: Blastn
[2024-01-24 12:40:38,600] [INFO] Running command: blastn -query GCF_028863365.1_ASM2886336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eb2d3bd-9871-416f-9940-ebe8a481763a/dqc_reference/reference_markers_gtdb.fasta -out GCF_028863365.1_ASM2886336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:40,759] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:40,764] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:40,764] [INFO] Target genome list was writen to GCF_028863365.1_ASM2886336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:40,773] [INFO] Task started: fastANI
[2024-01-24 12:40:40,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f9a0b0-6ff3-4b3b-87a2-dc829c2e5ef2/GCF_028863365.1_ASM2886336v1_genomic.fna.gz --refList GCF_028863365.1_ASM2886336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028863365.1_ASM2886336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:05,664] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:05,685] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:05,686] [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_001418645.1	s__Streptomyces neyagawaensis	99.5801	2249	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	conclusive
GCF_001419765.1	s__Streptomyces torulosus	95.3903	2139	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
GCF_900290235.1	s__Streptomyces sp900290235	95.2709	2623	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	96.28	96.28	0.86	0.86	2	-
GCF_001418475.1	s__Streptomyces ossamyceticus	94.7663	2091	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6547	98.97	98.97	0.90	0.90	2	-
GCF_009857135.1	s__Streptomyces sp009857135	93.42	2139	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	87.8926	2295	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_900114955.1	s__Streptomyces sp900114955	87.5349	2238	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	87.4458	2187	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.1451	1995	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	83.7587	1753	3271	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:05,688] [INFO] GTDB search result was written to GCF_028863365.1_ASM2886336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:05,689] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:05,693] [INFO] DFAST_QC result json was written to GCF_028863365.1_ASM2886336v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:05,693] [INFO] DFAST_QC completed!
[2024-01-24 12:41:05,693] [INFO] Total running time: 0h3m58s