[2024-01-24 12:23:03,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference
[2024-01-24 12:23:05,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,258] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg305f280d-082e-4e24-b387-7434b070cb50/GCF_019599145.1_ASM1959914v1_genomic.fna.gz | prodigal -d GCF_019599145.1_ASM1959914v1_genomic.fna/cds.fna -a GCF_019599145.1_ASM1959914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:40,632] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:40,633] [INFO] Task started: HMMsearch
[2024-01-24 12:23:40,633] [INFO] Running command: hmmsearch --tblout GCF_019599145.1_ASM1959914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference/reference_markers.hmm GCF_019599145.1_ASM1959914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:41,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:41,036] [INFO] Found 6/6 markers.
[2024-01-24 12:23:41,117] [INFO] Query marker FASTA was written to GCF_019599145.1_ASM1959914v1_genomic.fna/markers.fasta
[2024-01-24 12:23:41,118] [INFO] Task started: Blastn
[2024-01-24 12:23:41,118] [INFO] Running command: blastn -query GCF_019599145.1_ASM1959914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference/reference_markers.fasta -out GCF_019599145.1_ASM1959914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:42,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:42,370] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:42,370] [INFO] Target genome list was writen to GCF_019599145.1_ASM1959914v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:42,376] [INFO] Task started: fastANI
[2024-01-24 12:23:42,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg305f280d-082e-4e24-b387-7434b070cb50/GCF_019599145.1_ASM1959914v1_genomic.fna.gz --refList GCF_019599145.1_ASM1959914v1_genomic.fna/target_genomes.txt --output GCF_019599145.1_ASM1959914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:18,315] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:18,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:18,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:18,340] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:18,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:18,341] [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	93.2103	2675	3516	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	92.9249	2709	3516	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	90.3249	2336	3516	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	90.261	2421	3516	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	90.2414	2335	3516	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	90.1121	2337	3516	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	89.9764	2512	3516	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	89.1474	2243	3516	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	87.6265	2343	3516	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.5566	1903	3516	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	87.39	1666	3516	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.3363	2298	3516	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.0671	2001	3516	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	82.9091	1688	3516	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:18,342] [INFO] DFAST Taxonomy check result was written to GCF_019599145.1_ASM1959914v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:18,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:18,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:18,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference/checkm_data
[2024-01-24 12:24:18,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:18,440] [INFO] Task started: CheckM
[2024-01-24 12:24:18,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019599145.1_ASM1959914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019599145.1_ASM1959914v1_genomic.fna/checkm_input GCF_019599145.1_ASM1959914v1_genomic.fna/checkm_result
[2024-01-24 12:27:00,190] [INFO] Task succeeded: CheckM
[2024-01-24 12:27:00,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 12:27:00,223] [INFO] ===== Completeness check finished =====
[2024-01-24 12:27:00,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:27:00,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019599145.1_ASM1959914v1_genomic.fna/markers.fasta)
[2024-01-24 12:27:00,224] [INFO] Task started: Blastn
[2024-01-24 12:27:00,224] [INFO] Running command: blastn -query GCF_019599145.1_ASM1959914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f2700e8-c554-47d7-8d82-3112ea08b916/dqc_reference/reference_markers_gtdb.fasta -out GCF_019599145.1_ASM1959914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:02,228] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:02,233] [INFO] Selected 13 target genomes.
[2024-01-24 12:27:02,233] [INFO] Target genome list was writen to GCF_019599145.1_ASM1959914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:27:02,274] [INFO] Task started: fastANI
[2024-01-24 12:27:02,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg305f280d-082e-4e24-b387-7434b070cb50/GCF_019599145.1_ASM1959914v1_genomic.fna.gz --refList GCF_019599145.1_ASM1959914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019599145.1_ASM1959914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:27:35,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:35,286] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:27:35,286] [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_000772895.1	s__Streptomyces galbus_A	96.0841	2737	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114955.1	s__Streptomyces sp900114955	93.0366	2614	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_014203845.1	s__Streptomyces scabiei_E	92.657	2505	3516	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	90.32	2337	3516	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	90.3002	2215	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	90.2981	2416	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383595.1	s__Streptomyces bottropensis	90.2114	2339	3516	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	89.9836	2511	3516	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	89.1491	2243	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419765.1	s__Streptomyces torulosus	87.5609	1900	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
GCF_001418645.1	s__Streptomyces neyagawaensis	87.4073	1663	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_000746395.1	s__Streptomyces mirabilis_A	83.9843	1978	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362785.1	s__Streptomyces sp013362785	83.3266	1498	3516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:27:35,288] [INFO] GTDB search result was written to GCF_019599145.1_ASM1959914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:27:35,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:27:35,293] [INFO] DFAST_QC result json was written to GCF_019599145.1_ASM1959914v1_genomic.fna/dqc_result.json
[2024-01-24 12:27:35,293] [INFO] DFAST_QC completed!
[2024-01-24 12:27:35,294] [INFO] Total running time: 0h4m31s