[2024-01-24 12:31:19,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:19,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:19,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference
[2024-01-24 12:31:20,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:20,897] [INFO] Task started: Prodigal
[2024-01-24 12:31:20,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9e0cc03-673b-4753-a284-3cdb239a5fcc/GCF_000993785.3_ASM99378v3_genomic.fna.gz | prodigal -d GCF_000993785.3_ASM99378v3_genomic.fna/cds.fna -a GCF_000993785.3_ASM99378v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:40,593] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:40,594] [INFO] Task started: HMMsearch
[2024-01-24 12:31:40,594] [INFO] Running command: hmmsearch --tblout GCF_000993785.3_ASM99378v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference/reference_markers.hmm GCF_000993785.3_ASM99378v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:40,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:40,860] [INFO] Found 6/6 markers.
[2024-01-24 12:31:40,905] [INFO] Query marker FASTA was written to GCF_000993785.3_ASM99378v3_genomic.fna/markers.fasta
[2024-01-24 12:31:40,905] [INFO] Task started: Blastn
[2024-01-24 12:31:40,905] [INFO] Running command: blastn -query GCF_000993785.3_ASM99378v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference/reference_markers.fasta -out GCF_000993785.3_ASM99378v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:42,169] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:42,173] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:42,174] [INFO] Target genome list was writen to GCF_000993785.3_ASM99378v3_genomic.fna/target_genomes.txt
[2024-01-24 12:31:42,183] [INFO] Task started: fastANI
[2024-01-24 12:31:42,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9e0cc03-673b-4753-a284-3cdb239a5fcc/GCF_000993785.3_ASM99378v3_genomic.fna.gz --refList GCF_000993785.3_ASM99378v3_genomic.fna/target_genomes.txt --output GCF_000993785.3_ASM99378v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:11,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:11,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:11,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:11,584] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:11,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:11,584] [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 xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	100.0	1987	1987	95	conclusive
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.5042	1025	1987	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.4622	935	1987	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	80.8616	1056	1987	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	80.6711	1042	1987	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	80.566	1065	1987	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	80.5499	942	1987	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	80.4585	1093	1987	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	80.417	936	1987	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.3978	926	1987	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.8849	946	1987	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.771	784	1987	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.7556	900	1987	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	79.7426	849	1987	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.6103	956	1987	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	79.4987	956	1987	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	79.4613	929	1987	95	below_threshold
Streptomyces chilikensis	strain=RC 1830	GCA_001642695.2	1194079	1194079	type	True	79.3924	870	1987	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	79.2999	935	1987	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	79.2408	970	1987	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	78.6332	765	1987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,586] [INFO] DFAST Taxonomy check result was written to GCF_000993785.3_ASM99378v3_genomic.fna/tc_result.tsv
[2024-01-24 12:32:11,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:11,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:11,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference/checkm_data
[2024-01-24 12:32:11,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:11,642] [INFO] Task started: CheckM
[2024-01-24 12:32:11,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000993785.3_ASM99378v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000993785.3_ASM99378v3_genomic.fna/checkm_input GCF_000993785.3_ASM99378v3_genomic.fna/checkm_result
[2024-01-24 12:34:02,317] [INFO] Task succeeded: CheckM
[2024-01-24 12:34:02,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:34:02,339] [INFO] ===== Completeness check finished =====
[2024-01-24 12:34:02,339] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:34:02,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000993785.3_ASM99378v3_genomic.fna/markers.fasta)
[2024-01-24 12:34:02,339] [INFO] Task started: Blastn
[2024-01-24 12:34:02,339] [INFO] Running command: blastn -query GCF_000993785.3_ASM99378v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg18c56730-8fa8-4b7d-81f9-281f1484b33b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000993785.3_ASM99378v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:04,333] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:04,336] [INFO] Selected 18 target genomes.
[2024-01-24 12:34:04,336] [INFO] Target genome list was writen to GCF_000993785.3_ASM99378v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:34:04,363] [INFO] Task started: fastANI
[2024-01-24 12:34:04,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9e0cc03-673b-4753-a284-3cdb239a5fcc/GCF_000993785.3_ASM99378v3_genomic.fna.gz --refList GCF_000993785.3_ASM99378v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000993785.3_ASM99378v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:30,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:30,814] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:30,814] [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_000993785.3	s__Streptomyces xiamenensis	100.0	1987	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	97.97	0.94	0.91	3	conclusive
GCF_900116145.1	s__Streptomyces harbinensis	88.8803	1555	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	-
GCF_004348415.1	s__Streptomyces hainanensis	81.4476	1034	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.3917	938	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	81.233	1062	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	80.8271	1043	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984575.1	s__Streptomyces sp001984575	80.7734	1127	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335015.1	s__Streptomyces sedi	80.6735	1042	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011421595.1	s__Streptomyces sp011421595	80.5998	935	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	80.5803	1062	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719135.1	s__Streptomyces avicenniae	80.563	1011	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974485.1	s__Streptomyces sp000974485	80.4205	1064	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779715.1	s__Streptomyces chumphonensis	79.8055	839	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726235.1	s__Streptomyces sp012726235	79.712	881	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010384365.1	s__Streptomyces sp010384365	79.3029	890	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
GCF_016741935.1	s__Streptomyces sp016741935	79.2612	1043	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_002813165.1	s__Kitasatospora sp002813165	78.4513	880	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.28	97.28	0.90	0.90	2	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	78.2971	886	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:30,815] [INFO] GTDB search result was written to GCF_000993785.3_ASM99378v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:30,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:30,820] [INFO] DFAST_QC result json was written to GCF_000993785.3_ASM99378v3_genomic.fna/dqc_result.json
[2024-01-24 12:34:30,820] [INFO] DFAST_QC completed!
[2024-01-24 12:34:30,820] [INFO] Total running time: 0h3m11s