[2024-01-24 14:30:16,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference
[2024-01-24 14:30:18,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,143] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg0659f4cd-e862-4811-91b7-25f78452d57f/GCF_014873495.1_ASM1487349v1_genomic.fna.gz | prodigal -d GCF_014873495.1_ASM1487349v1_genomic.fna/cds.fna -a GCF_014873495.1_ASM1487349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:53,323] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:53,324] [INFO] Task started: HMMsearch
[2024-01-24 14:30:53,324] [INFO] Running command: hmmsearch --tblout GCF_014873495.1_ASM1487349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference/reference_markers.hmm GCF_014873495.1_ASM1487349v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:53,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:53,771] [INFO] Found 6/6 markers.
[2024-01-24 14:30:53,858] [INFO] Query marker FASTA was written to GCF_014873495.1_ASM1487349v1_genomic.fna/markers.fasta
[2024-01-24 14:30:53,858] [INFO] Task started: Blastn
[2024-01-24 14:30:53,858] [INFO] Running command: blastn -query GCF_014873495.1_ASM1487349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference/reference_markers.fasta -out GCF_014873495.1_ASM1487349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:55,155] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:55,158] [INFO] Selected 10 target genomes.
[2024-01-24 14:30:55,159] [INFO] Target genome list was writen to GCF_014873495.1_ASM1487349v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:55,163] [INFO] Task started: fastANI
[2024-01-24 14:30:55,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg0659f4cd-e862-4811-91b7-25f78452d57f/GCF_014873495.1_ASM1487349v1_genomic.fna.gz --refList GCF_014873495.1_ASM1487349v1_genomic.fna/target_genomes.txt --output GCF_014873495.1_ASM1487349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:24,831] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:24,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:24,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:24,841] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:24,841] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:31:24,842] [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 stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	100.0	3495	3498	95	inconclusive
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	96.7234	2549	3498	95	inconclusive
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	96.7037	2543	3498	95	inconclusive
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	90.5684	2329	3498	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	90.2055	2359	3498	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	90.1741	2472	3498	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	90.1049	2525	3498	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.6775	1947	3498	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.6086	2335	3498	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.0576	1979	3498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:24,843] [INFO] DFAST Taxonomy check result was written to GCF_014873495.1_ASM1487349v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:24,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:24,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:24,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference/checkm_data
[2024-01-24 14:31:24,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:24,942] [INFO] Task started: CheckM
[2024-01-24 14:31:24,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873495.1_ASM1487349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873495.1_ASM1487349v1_genomic.fna/checkm_input GCF_014873495.1_ASM1487349v1_genomic.fna/checkm_result
[2024-01-24 14:34:01,898] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:01,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:34:01,930] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:01,931] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:01,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873495.1_ASM1487349v1_genomic.fna/markers.fasta)
[2024-01-24 14:34:01,932] [INFO] Task started: Blastn
[2024-01-24 14:34:01,932] [INFO] Running command: blastn -query GCF_014873495.1_ASM1487349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05e7c9d7-473e-4c24-97d3-9ca5e016f40b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873495.1_ASM1487349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:04,078] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:04,082] [INFO] Selected 10 target genomes.
[2024-01-24 14:34:04,082] [INFO] Target genome list was writen to GCF_014873495.1_ASM1487349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:04,093] [INFO] Task started: fastANI
[2024-01-24 14:34:04,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg0659f4cd-e862-4811-91b7-25f78452d57f/GCF_014873495.1_ASM1487349v1_genomic.fna.gz --refList GCF_014873495.1_ASM1487349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873495.1_ASM1487349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:35,469] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:35,485] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:35,485] [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_014873495.1	s__Streptomyces stelliscabiei	100.0	3496	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	conclusive
GCF_000383595.1	s__Streptomyces bottropensis	96.7244	2549	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_000091305.1	s__Streptomyces scabiei	92.4027	2723	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	97.09	0.94	0.86	16	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	91.2946	2317	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_018927715.1	s__Streptomyces brasiliscabiei	90.5731	2328	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114955.1	s__Streptomyces sp900114955	90.1794	2410	3498	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	90.1678	2368	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772895.1	s__Streptomyces galbus_A	90.1026	2418	3498	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	89.9631	2362	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_001419765.1	s__Streptomyces torulosus	87.7118	1942	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:35,487] [INFO] GTDB search result was written to GCF_014873495.1_ASM1487349v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:35,487] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:35,490] [INFO] DFAST_QC result json was written to GCF_014873495.1_ASM1487349v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:35,490] [INFO] DFAST_QC completed!
[2024-01-24 14:34:35,490] [INFO] Total running time: 0h4m19s