[2024-01-24 12:13:06,292] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:06,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:06,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference
[2024-01-24 12:13:07,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,491] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgf14b38a3-e44f-4491-b57c-cc490a716a49/GCF_002911015.1_ASM291101v1_genomic.fna.gz | prodigal -d GCF_002911015.1_ASM291101v1_genomic.fna/cds.fna -a GCF_002911015.1_ASM291101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:31,830] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:31,831] [INFO] Task started: HMMsearch
[2024-01-24 12:13:31,831] [INFO] Running command: hmmsearch --tblout GCF_002911015.1_ASM291101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference/reference_markers.hmm GCF_002911015.1_ASM291101v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:32,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:32,139] [INFO] Found 6/6 markers.
[2024-01-24 12:13:32,203] [INFO] Query marker FASTA was written to GCF_002911015.1_ASM291101v1_genomic.fna/markers.fasta
[2024-01-24 12:13:32,203] [INFO] Task started: Blastn
[2024-01-24 12:13:32,204] [INFO] Running command: blastn -query GCF_002911015.1_ASM291101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference/reference_markers.fasta -out GCF_002911015.1_ASM291101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:33,592] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:33,596] [INFO] Selected 22 target genomes.
[2024-01-24 12:13:33,596] [INFO] Target genome list was writen to GCF_002911015.1_ASM291101v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:33,613] [INFO] Task started: fastANI
[2024-01-24 12:13:33,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgf14b38a3-e44f-4491-b57c-cc490a716a49/GCF_002911015.1_ASM291101v1_genomic.fna.gz --refList GCF_002911015.1_ASM291101v1_genomic.fna/target_genomes.txt --output GCF_002911015.1_ASM291101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:21,703] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:21,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:21,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:21,719] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:21,719] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:14:21,719] [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 populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	100.0	3049	3063	95	inconclusive
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	95.1705	2516	3063	95	inconclusive
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	86.5083	2027	3063	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	86.4234	1720	3063	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	86.0258	1975	3063	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	85.8547	2012	3063	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	85.2367	1819	3063	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	85.2357	1830	3063	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	85.0902	1898	3063	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.961	1891	3063	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	83.9357	1831	3063	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	83.8558	1846	3063	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.774	1620	3063	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	83.6119	1629	3063	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.5967	1565	3063	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.5402	1761	3063	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	83.4473	1726	3063	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.441	1799	3063	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.3336	1588	3063	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	81.8611	1486	3063	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.6856	1497	3063	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	81.3104	1383	3063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:21,721] [INFO] DFAST Taxonomy check result was written to GCF_002911015.1_ASM291101v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:21,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:21,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:21,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference/checkm_data
[2024-01-24 12:14:21,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:21,803] [INFO] Task started: CheckM
[2024-01-24 12:14:21,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002911015.1_ASM291101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002911015.1_ASM291101v1_genomic.fna/checkm_input GCF_002911015.1_ASM291101v1_genomic.fna/checkm_result
[2024-01-24 12:16:23,067] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:23,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:23,091] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:23,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:23,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002911015.1_ASM291101v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:23,092] [INFO] Task started: Blastn
[2024-01-24 12:16:23,092] [INFO] Running command: blastn -query GCF_002911015.1_ASM291101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d927079-0ebd-40fd-a3ff-152bb2908ae9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002911015.1_ASM291101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:25,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:25,405] [INFO] Selected 18 target genomes.
[2024-01-24 12:16:25,405] [INFO] Target genome list was writen to GCF_002911015.1_ASM291101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:25,416] [INFO] Task started: fastANI
[2024-01-24 12:16:25,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgf14b38a3-e44f-4491-b57c-cc490a716a49/GCF_002911015.1_ASM291101v1_genomic.fna.gz --refList GCF_002911015.1_ASM291101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002911015.1_ASM291101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:06,437] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:06,452] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:06,452] [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_002911015.1	s__Streptomyces populi	100.0	3049	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	conclusive
GCF_000725495.1	s__Streptomyces aureus_B	91.5994	2415	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078175.1	s__Streptomyces sp002078175	87.5432	2019	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.16	97.16	0.90	0.90	2	-
GCF_002300165.1	s__Streptomyces sp002300165	86.6595	1905	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.35	96.35	0.87	0.87	2	-
GCF_014645835.1	s__Streptomyces albiflavescens	86.514	2026	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002946835.1	s__Streptomyces dengpaensis	86.4203	1721	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014650275.1	s__Streptomyces mirabilis	86.0466	1972	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_012273535.1	s__Streptomyces sp002846625	85.84	2001	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
GCF_001514115.1	s__Streptomyces olivochromogenes	85.8366	2016	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_008042115.1	s__Streptomyces sp008042115	85.509	1900	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009765.2	s__Streptomyces avermitilis	85.2328	1830	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.91	0.98	0.92	9	-
GCF_008369065.1	s__Streptomyces sp008369065	84.0838	1699	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	83.934	1832	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954775.1	s__Streptomyces geranii	83.29	1597	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	81.7525	1474	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014649755.1	s__Streptomyces litmocidini	81.6462	1439	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_014649855.1	s__Streptomyces roseolus	81.5627	1370	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	81.5568	1483	3063	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:06,454] [INFO] GTDB search result was written to GCF_002911015.1_ASM291101v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:06,454] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:06,460] [INFO] DFAST_QC result json was written to GCF_002911015.1_ASM291101v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:06,461] [INFO] DFAST_QC completed!
[2024-01-24 12:17:06,461] [INFO] Total running time: 0h4m0s