[2024-01-24 14:46:55,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference
[2024-01-24 14:46:58,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,023] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg77a561c9-0e12-435f-8251-0ec30d83faa4/GCF_020010925.1_ASM2001092v1_genomic.fna.gz | prodigal -d GCF_020010925.1_ASM2001092v1_genomic.fna/cds.fna -a GCF_020010925.1_ASM2001092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:29,863] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:29,863] [INFO] Task started: HMMsearch
[2024-01-24 14:47:29,864] [INFO] Running command: hmmsearch --tblout GCF_020010925.1_ASM2001092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference/reference_markers.hmm GCF_020010925.1_ASM2001092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:30,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:30,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77a561c9-0e12-435f-8251-0ec30d83faa4/GCF_020010925.1_ASM2001092v1_genomic.fna.gz]
[2024-01-24 14:47:30,376] [INFO] Query marker FASTA was written to GCF_020010925.1_ASM2001092v1_genomic.fna/markers.fasta
[2024-01-24 14:47:30,377] [INFO] Task started: Blastn
[2024-01-24 14:47:30,377] [INFO] Running command: blastn -query GCF_020010925.1_ASM2001092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference/reference_markers.fasta -out GCF_020010925.1_ASM2001092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:31,654] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:31,658] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:31,658] [INFO] Target genome list was writen to GCF_020010925.1_ASM2001092v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:31,665] [INFO] Task started: fastANI
[2024-01-24 14:47:31,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a561c9-0e12-435f-8251-0ec30d83faa4/GCF_020010925.1_ASM2001092v1_genomic.fna.gz --refList GCF_020010925.1_ASM2001092v1_genomic.fna/target_genomes.txt --output GCF_020010925.1_ASM2001092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:13,036] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:13,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:13,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:13,049] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:13,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:13,050] [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 brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	98.9965	2853	3532	95	conclusive
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	92.4218	2478	3532	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	90.6951	2484	3532	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	90.5501	2467	3532	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	90.4038	2202	3532	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	90.3931	2519	3532	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	90.3581	2216	3532	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	89.1879	2154	3532	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.6145	1831	3532	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.5352	2225	3532	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.6201	1776	3532	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	83.5193	1756	3532	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	83.5054	1725	3532	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	83.1451	1592	3532	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	83.0874	1481	3532	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	82.7979	1439	3532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:13,052] [INFO] DFAST Taxonomy check result was written to GCF_020010925.1_ASM2001092v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:13,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:13,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:13,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference/checkm_data
[2024-01-24 14:48:13,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:13,152] [INFO] Task started: CheckM
[2024-01-24 14:48:13,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020010925.1_ASM2001092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020010925.1_ASM2001092v1_genomic.fna/checkm_input GCF_020010925.1_ASM2001092v1_genomic.fna/checkm_result
[2024-01-24 14:51:00,944] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:00,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:00,973] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:00,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:00,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020010925.1_ASM2001092v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:00,975] [INFO] Task started: Blastn
[2024-01-24 14:51:00,975] [INFO] Running command: blastn -query GCF_020010925.1_ASM2001092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133fb38d-5a5a-486a-baf5-146659b99e2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_020010925.1_ASM2001092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:02,970] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:02,973] [INFO] Selected 16 target genomes.
[2024-01-24 14:51:02,974] [INFO] Target genome list was writen to GCF_020010925.1_ASM2001092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:02,984] [INFO] Task started: fastANI
[2024-01-24 14:51:02,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a561c9-0e12-435f-8251-0ec30d83faa4/GCF_020010925.1_ASM2001092v1_genomic.fna.gz --refList GCF_020010925.1_ASM2001092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020010925.1_ASM2001092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:43,537] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:43,568] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:43,569] [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_018927715.1	s__Streptomyces brasiliscabiei	99.0009	2853	3532	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_009184865.1	s__Streptomyces phaeolivaceus	92.4282	2477	3532	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	90.6919	2143	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_014873495.1	s__Streptomyces stelliscabiei	90.5639	2463	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_900114955.1	s__Streptomyces sp900114955	90.5106	2445	3532	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	90.3962	2260	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_000383595.1	s__Streptomyces bottropensis	90.3909	2204	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_000772895.1	s__Streptomyces galbus_A	90.3225	2382	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598475.1	s__Streptomyces adelaidensis	89.1518	2160	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418645.1	s__Streptomyces neyagawaensis	87.4066	1599	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCA_002027195.1	s__Streptomyces sp002027195	84.5366	1674	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	83.5125	1757	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364255.1	s__Streptomyces seoulensis_A	82.8966	1608	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921115.1	s__Streptomyces actuosus_A	82.71	1524	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982015.1	s__Streptomyces sp002982015	81.4066	1046	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005405945.1	s__Streptomyces violaceusniger	79.9361	1557	3532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:43,570] [INFO] GTDB search result was written to GCF_020010925.1_ASM2001092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:43,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:43,576] [INFO] DFAST_QC result json was written to GCF_020010925.1_ASM2001092v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:43,577] [INFO] DFAST_QC completed!
[2024-01-24 14:51:43,577] [INFO] Total running time: 0h4m49s