[2024-01-24 12:53:41,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference
[2024-01-24 12:53:43,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:43,091] [INFO] Task started: Prodigal
[2024-01-24 12:53:43,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg429a90ce-4c94-4cc6-a3d1-396bbbf8ef69/GCF_002261115.1_ASM226111v1_genomic.fna.gz | prodigal -d GCF_002261115.1_ASM226111v1_genomic.fna/cds.fna -a GCF_002261115.1_ASM226111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:10,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:10,908] [INFO] Task started: HMMsearch
[2024-01-24 12:54:10,908] [INFO] Running command: hmmsearch --tblout GCF_002261115.1_ASM226111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference/reference_markers.hmm GCF_002261115.1_ASM226111v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:11,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:11,319] [INFO] Found 6/6 markers.
[2024-01-24 12:54:11,408] [INFO] Query marker FASTA was written to GCF_002261115.1_ASM226111v1_genomic.fna/markers.fasta
[2024-01-24 12:54:11,409] [INFO] Task started: Blastn
[2024-01-24 12:54:11,409] [INFO] Running command: blastn -query GCF_002261115.1_ASM226111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference/reference_markers.fasta -out GCF_002261115.1_ASM226111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:12,826] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:12,831] [INFO] Selected 18 target genomes.
[2024-01-24 12:54:12,831] [INFO] Target genome list was writen to GCF_002261115.1_ASM226111v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:12,838] [INFO] Task started: fastANI
[2024-01-24 12:54:12,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg429a90ce-4c94-4cc6-a3d1-396bbbf8ef69/GCF_002261115.1_ASM226111v1_genomic.fna.gz --refList GCF_002261115.1_ASM226111v1_genomic.fna/target_genomes.txt --output GCF_002261115.1_ASM226111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:51,374] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:51,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:51,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:51,453] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:51,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:51,453] [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 kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	99.9995	3079	3085	95	conclusive
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	86.603	1691	3085	95	below_threshold
Streptomyces piniterrae	strain=jys28	GCA_005048155.1	2571125	2571125	type	True	86.4635	1689	3085	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	86.3601	1747	3085	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	86.3199	1662	3085	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	86.1652	1781	3085	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	86.1567	1729	3085	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	86.1071	1788	3085	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	86.0671	1718	3085	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	86.0145	1681	3085	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	85.9009	1642	3085	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.8619	1677	3085	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	85.6623	1736	3085	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.7857	1281	3085	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.9412	1704	3085	95	below_threshold
Streptomyces chrestomyceticus	strain=NBRC 13444	GCA_003865135.1	68185	68185	type	True	83.76	1711	3085	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.7192	1716	3085	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.6873	1704	3085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:51,455] [INFO] DFAST Taxonomy check result was written to GCF_002261115.1_ASM226111v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:51,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:51,456] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:51,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference/checkm_data
[2024-01-24 12:54:51,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:51,552] [INFO] Task started: CheckM
[2024-01-24 12:54:51,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002261115.1_ASM226111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002261115.1_ASM226111v1_genomic.fna/checkm_input GCF_002261115.1_ASM226111v1_genomic.fna/checkm_result
[2024-01-24 12:56:42,778] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:42,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:42,807] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:42,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:42,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002261115.1_ASM226111v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:42,808] [INFO] Task started: Blastn
[2024-01-24 12:56:42,808] [INFO] Running command: blastn -query GCF_002261115.1_ASM226111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cacd73b-fbd8-4a38-9c20-01a94c5e33ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_002261115.1_ASM226111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:45,203] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:45,208] [INFO] Selected 16 target genomes.
[2024-01-24 12:56:45,208] [INFO] Target genome list was writen to GCF_002261115.1_ASM226111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:45,221] [INFO] Task started: fastANI
[2024-01-24 12:56:45,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg429a90ce-4c94-4cc6-a3d1-396bbbf8ef69/GCF_002261115.1_ASM226111v1_genomic.fna.gz --refList GCF_002261115.1_ASM226111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002261115.1_ASM226111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:57:20,494] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:20,565] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:57:20,566] [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
GCA_000720995.1	s__Streptomyces celluloflavus	99.0521	2714	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.24	98.62	0.95	0.89	4	conclusive
GCF_003389455.1	s__Streptomyces inhibens	86.565	1697	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048155.1	s__Streptomyces piniterrae	86.4825	1687	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	86.3298	1661	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	86.127	1785	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811595.1	s__Streptomyces libani	86.0754	1809	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_008704855.1	s__Streptomyces platensis	86.0727	1716	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_004122735.1	s__Streptomyces sioyaensis	86.0374	1557	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_900187385.1	s__Streptomyces sp900187385	85.906	1695	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_014646275.1	s__Streptomyces kronopolitis	85.905	1642	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648695.1	s__Streptomyces albospinus	85.6547	1737	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834125.1	s__Streptomyces sp009834125	85.6017	1761	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294335.1	s__Streptomyces chattanoogensis	85.5567	1695	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	97.46	0.90	0.90	2	-
GCF_002082195.1	s__Streptomyces gilvosporeus	85.3101	1647	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_000935125.1	s__Streptomyces natalensis	85.2358	1657	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_003865135.1	s__Streptomyces chrestomyceticus	83.7442	1713	3085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.95	95.89	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:57:20,567] [INFO] GTDB search result was written to GCF_002261115.1_ASM226111v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:57:20,568] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:57:20,572] [INFO] DFAST_QC result json was written to GCF_002261115.1_ASM226111v1_genomic.fna/dqc_result.json
[2024-01-24 12:57:20,573] [INFO] DFAST_QC completed!
[2024-01-24 12:57:20,573] [INFO] Total running time: 0h3m39s