[2024-01-25 19:53:35,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference
[2024-01-25 19:53:36,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,740] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg93a2f1e4-771a-4bbe-876c-789070368568/GCF_022385335.1_ASM2238533v1_genomic.fna.gz | prodigal -d GCF_022385335.1_ASM2238533v1_genomic.fna/cds.fna -a GCF_022385335.1_ASM2238533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:04,770] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:04,771] [INFO] Task started: HMMsearch
[2024-01-25 19:54:04,771] [INFO] Running command: hmmsearch --tblout GCF_022385335.1_ASM2238533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference/reference_markers.hmm GCF_022385335.1_ASM2238533v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:05,207] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:05,209] [INFO] Found 6/6 markers.
[2024-01-25 19:54:05,288] [INFO] Query marker FASTA was written to GCF_022385335.1_ASM2238533v1_genomic.fna/markers.fasta
[2024-01-25 19:54:05,288] [INFO] Task started: Blastn
[2024-01-25 19:54:05,288] [INFO] Running command: blastn -query GCF_022385335.1_ASM2238533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference/reference_markers.fasta -out GCF_022385335.1_ASM2238533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:06,537] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:06,540] [INFO] Selected 11 target genomes.
[2024-01-25 19:54:06,540] [INFO] Target genome list was writen to GCF_022385335.1_ASM2238533v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:06,551] [INFO] Task started: fastANI
[2024-01-25 19:54:06,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg93a2f1e4-771a-4bbe-876c-789070368568/GCF_022385335.1_ASM2238533v1_genomic.fna.gz --refList GCF_022385335.1_ASM2238533v1_genomic.fna/target_genomes.txt --output GCF_022385335.1_ASM2238533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:38,079] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:38,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:38,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:38,087] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:38,088] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:38,088] [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 deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	100.0	3365	3367	95	conclusive
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	93.6476	2775	3367	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	90.6864	2369	3367	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	90.5963	2445	3367	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	90.1765	2317	3367	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	90.1698	2306	3367	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	90.1219	2507	3367	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	89.1753	2211	3367	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.8309	1879	3367	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.5923	2264	3367	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.3575	2067	3367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:38,089] [INFO] DFAST Taxonomy check result was written to GCF_022385335.1_ASM2238533v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:38,090] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:38,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:38,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference/checkm_data
[2024-01-25 19:54:38,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:38,182] [INFO] Task started: CheckM
[2024-01-25 19:54:38,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022385335.1_ASM2238533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022385335.1_ASM2238533v1_genomic.fna/checkm_input GCF_022385335.1_ASM2238533v1_genomic.fna/checkm_result
[2024-01-25 19:57:41,867] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:41,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-25 19:57:41,897] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:41,897] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:41,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022385335.1_ASM2238533v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:41,907] [INFO] Task started: Blastn
[2024-01-25 19:57:41,907] [INFO] Running command: blastn -query GCF_022385335.1_ASM2238533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8710ba86-614e-490e-8365-0d83c22f3175/dqc_reference/reference_markers_gtdb.fasta -out GCF_022385335.1_ASM2238533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:43,994] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:44,002] [INFO] Selected 9 target genomes.
[2024-01-25 19:57:44,002] [INFO] Target genome list was writen to GCF_022385335.1_ASM2238533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:44,008] [INFO] Task started: fastANI
[2024-01-25 19:57:44,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg93a2f1e4-771a-4bbe-876c-789070368568/GCF_022385335.1_ASM2238533v1_genomic.fna.gz --refList GCF_022385335.1_ASM2238533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022385335.1_ASM2238533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:08,858] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:08,864] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:58:08,865] [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_900114955.1	s__Streptomyces sp900114955	93.8553	2628	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_000772895.1	s__Streptomyces galbus_A	93.1126	2631	3367	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	92.7465	2432	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_018927715.1	s__Streptomyces brasiliscabiei	90.6796	2370	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	90.5812	2448	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	90.2576	2204	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_000383595.1	s__Streptomyces bottropensis	90.1951	2314	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_014873495.1	s__Streptomyces stelliscabiei	90.1274	2506	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_016598475.1	s__Streptomyces adelaidensis	89.2036	2207	3367	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:08,866] [INFO] GTDB search result was written to GCF_022385335.1_ASM2238533v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:08,866] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:08,874] [INFO] DFAST_QC result json was written to GCF_022385335.1_ASM2238533v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:08,874] [INFO] DFAST_QC completed!
[2024-01-25 19:58:08,874] [INFO] Total running time: 0h4m33s