[2024-01-24 11:12:27,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference
[2024-01-24 11:12:29,147] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,148] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ea9f286-8cb8-4ca4-86b0-b1de333a6d40/GCF_016906185.1_ASM1690618v1_genomic.fna.gz | prodigal -d GCF_016906185.1_ASM1690618v1_genomic.fna/cds.fna -a GCF_016906185.1_ASM1690618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:52,333] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:52,333] [INFO] Task started: HMMsearch
[2024-01-24 11:12:52,333] [INFO] Running command: hmmsearch --tblout GCF_016906185.1_ASM1690618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference/reference_markers.hmm GCF_016906185.1_ASM1690618v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:52,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:52,821] [INFO] Found 6/6 markers.
[2024-01-24 11:12:52,884] [INFO] Query marker FASTA was written to GCF_016906185.1_ASM1690618v1_genomic.fna/markers.fasta
[2024-01-24 11:12:52,885] [INFO] Task started: Blastn
[2024-01-24 11:12:52,885] [INFO] Running command: blastn -query GCF_016906185.1_ASM1690618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference/reference_markers.fasta -out GCF_016906185.1_ASM1690618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:54,259] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:54,263] [INFO] Selected 14 target genomes.
[2024-01-24 11:12:54,263] [INFO] Target genome list was writen to GCF_016906185.1_ASM1690618v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:54,269] [INFO] Task started: fastANI
[2024-01-24 11:12:54,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea9f286-8cb8-4ca4-86b0-b1de333a6d40/GCF_016906185.1_ASM1690618v1_genomic.fna.gz --refList GCF_016906185.1_ASM1690618v1_genomic.fna/target_genomes.txt --output GCF_016906185.1_ASM1690618v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:22,877] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:22,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:22,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:22,892] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:22,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:22,893] [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 californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	100.0	2674	2676	95	conclusive
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	99.9736	2556	2676	95	conclusive
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	90.6071	2009	2676	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	90.5161	1794	2676	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	90.4534	1941	2676	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	90.307	2065	2676	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	90.2679	1945	2676	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	90.1855	2078	2676	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	90.1767	2039	2676	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	88.2957	1551	2676	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.3744	1574	2676	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5504	1388	2676	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	81.117	1379	2676	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.8909	1400	2676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:22,895] [INFO] DFAST Taxonomy check result was written to GCF_016906185.1_ASM1690618v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:22,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:22,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:22,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference/checkm_data
[2024-01-24 11:13:22,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:22,980] [INFO] Task started: CheckM
[2024-01-24 11:13:22,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016906185.1_ASM1690618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016906185.1_ASM1690618v1_genomic.fna/checkm_input GCF_016906185.1_ASM1690618v1_genomic.fna/checkm_result
[2024-01-24 11:15:33,372] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:33,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:33,404] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:33,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:33,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016906185.1_ASM1690618v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:33,405] [INFO] Task started: Blastn
[2024-01-24 11:15:33,405] [INFO] Running command: blastn -query GCF_016906185.1_ASM1690618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452f62d7-968b-4d15-a717-eca1d4945985/dqc_reference/reference_markers_gtdb.fasta -out GCF_016906185.1_ASM1690618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:35,489] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:35,494] [INFO] Selected 17 target genomes.
[2024-01-24 11:15:35,494] [INFO] Target genome list was writen to GCF_016906185.1_ASM1690618v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:35,507] [INFO] Task started: fastANI
[2024-01-24 11:15:35,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea9f286-8cb8-4ca4-86b0-b1de333a6d40/GCF_016906185.1_ASM1690618v1_genomic.fna.gz --refList GCF_016906185.1_ASM1690618v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016906185.1_ASM1690618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:09,899] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:09,925] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:09,925] [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_000717645.1	s__Streptomyces californicus	99.9736	2556	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.00	97.83	0.95	0.89	42	conclusive
GCF_001905905.1	s__Streptomyces sp001905905	92.0081	2021	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	90.7338	2020	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_003501885.1	s__Streptomyces globisporus_D	90.6535	1779	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_001687325.1	s__Streptomyces sp001687325	90.6453	1978	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002551355.1	s__Streptomyces sp002551355	90.616	1974	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901035.1	s__Streptomyces sp016901035	90.612	1807	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649555.1	s__Streptomyces globisporus	90.5984	2034	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_014648875.1	s__Streptomyces parvus	90.5948	2010	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCF_000718455.1	s__Streptomyces globisporus_A	90.5345	1927	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_014649035.1	s__Streptomyces sindenensis	90.4287	1944	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	-
GCF_014650675.1	s__Streptomyces anulatus	90.305	2065	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
GCF_018619185.1	s__Streptomyces sp018619185	90.2457	1810	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460065.1	s__Streptomyces griseus	90.1896	2035	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.49	99.03	0.95	0.93	10	-
GCF_002551245.1	s__Streptomyces sp002551245	90.1108	1768	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721175.1	s__Streptomyces anulatus_C	90.0092	1883	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.46	0.95	0.90	3	-
GCF_018866325.1	s__Streptomyces sp001895105	89.9782	1953	2676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:16:09,927] [INFO] GTDB search result was written to GCF_016906185.1_ASM1690618v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:09,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:09,932] [INFO] DFAST_QC result json was written to GCF_016906185.1_ASM1690618v1_genomic.fna/dqc_result.json
[2024-01-24 11:16:09,933] [INFO] DFAST_QC completed!
[2024-01-24 11:16:09,933] [INFO] Total running time: 0h3m42s