[2024-01-25 19:42:20,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:20,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:20,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference
[2024-01-25 19:42:21,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:21,716] [INFO] Task started: Prodigal
[2024-01-25 19:42:21,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg33be2bae-02b3-4552-8697-f2d7e30b16fa/GCF_014650235.1_ASM1465023v1_genomic.fna.gz | prodigal -d GCF_014650235.1_ASM1465023v1_genomic.fna/cds.fna -a GCF_014650235.1_ASM1465023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:44,728] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:44,728] [INFO] Task started: HMMsearch
[2024-01-25 19:42:44,728] [INFO] Running command: hmmsearch --tblout GCF_014650235.1_ASM1465023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference/reference_markers.hmm GCF_014650235.1_ASM1465023v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:45,046] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:45,047] [INFO] Found 6/6 markers.
[2024-01-25 19:42:45,110] [INFO] Query marker FASTA was written to GCF_014650235.1_ASM1465023v1_genomic.fna/markers.fasta
[2024-01-25 19:42:45,110] [INFO] Task started: Blastn
[2024-01-25 19:42:45,110] [INFO] Running command: blastn -query GCF_014650235.1_ASM1465023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference/reference_markers.fasta -out GCF_014650235.1_ASM1465023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:46,343] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:46,345] [INFO] Selected 21 target genomes.
[2024-01-25 19:42:46,345] [INFO] Target genome list was writen to GCF_014650235.1_ASM1465023v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:46,360] [INFO] Task started: fastANI
[2024-01-25 19:42:46,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg33be2bae-02b3-4552-8697-f2d7e30b16fa/GCF_014650235.1_ASM1465023v1_genomic.fna.gz --refList GCF_014650235.1_ASM1465023v1_genomic.fna/target_genomes.txt --output GCF_014650235.1_ASM1465023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:29,271] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:29,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:29,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:29,284] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:43:29,284] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:43:29,285] [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 violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	100.0	2941	2941	95	inconclusive
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	95.3076	2364	2941	95	inconclusive
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	93.7264	1924	2941	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	93.2117	2341	2941	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	93.1911	2414	2941	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	93.0339	2332	2941	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	92.9216	2129	2941	95	below_threshold
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	92.8484	2384	2941	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.4636	2323	2941	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.4587	2324	2941	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	91.9513	2033	2941	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.0492	2222	2941	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.7574	2297	2941	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	85.7566	2074	2941	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	85.7369	2062	2941	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.2001	1763	2941	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	84.9843	1579	2941	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	76.6209	652	2941	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	76.3889	534	2941	95	below_threshold
Aestuariimicrobium kwangyangense	strain=DSM 21549	GCA_000421525.1	396389	396389	type	True	76.095	202	2941	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	75.5931	404	2941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:29,286] [INFO] DFAST Taxonomy check result was written to GCF_014650235.1_ASM1465023v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:29,289] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:29,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:29,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference/checkm_data
[2024-01-25 19:43:29,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:29,369] [INFO] Task started: CheckM
[2024-01-25 19:43:29,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650235.1_ASM1465023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650235.1_ASM1465023v1_genomic.fna/checkm_input GCF_014650235.1_ASM1465023v1_genomic.fna/checkm_result
[2024-01-25 19:45:32,686] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:32,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:32,706] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:32,706] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:32,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650235.1_ASM1465023v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:32,707] [INFO] Task started: Blastn
[2024-01-25 19:45:32,707] [INFO] Running command: blastn -query GCF_014650235.1_ASM1465023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5446b67d-8361-4953-945b-3079fe84975f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650235.1_ASM1465023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:34,834] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:34,837] [INFO] Selected 15 target genomes.
[2024-01-25 19:45:34,837] [INFO] Target genome list was writen to GCF_014650235.1_ASM1465023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:34,860] [INFO] Task started: fastANI
[2024-01-25 19:45:34,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg33be2bae-02b3-4552-8697-f2d7e30b16fa/GCF_014650235.1_ASM1465023v1_genomic.fna.gz --refList GCF_014650235.1_ASM1465023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650235.1_ASM1465023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:11,302] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:11,311] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:11,312] [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_014204745.1	s__Streptomyces collinus	99.3633	2766	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	conclusive
GCF_000717055.1	s__Streptomyces iakyrus	95.3146	2363	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_001611795.1	s__Streptomyces qaidamensis	95.2704	2451	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_014202475.1	s__Streptomyces paradoxus	94.7566	2434	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803895.1	s__Streptomyces hawaiiensis	93.2197	2340	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014648995.1	s__Streptomyces massasporeus	93.1977	2414	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_014205055.1	s__Streptomyces luteogriseus	92.8561	2383	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_007655005.1	s__Streptomyces tibetensis	92.458	2324	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCA_000696115.1	s__Streptomyces olindensis	90.73	2272	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004187715.1	s__Streptomyces sp004187715	85.6333	1889	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.6204	2069	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	85.5882	1806	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_014650435.1	s__Streptomyces tendae	85.3054	1757	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003143855.1	s__Streptomyces sp003143855	85.2052	1675	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_000761215.1	s__Streptomyces glaucescens	85.0661	1739	2941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:11,316] [INFO] GTDB search result was written to GCF_014650235.1_ASM1465023v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:11,316] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:11,320] [INFO] DFAST_QC result json was written to GCF_014650235.1_ASM1465023v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:11,320] [INFO] DFAST_QC completed!
[2024-01-25 19:46:11,320] [INFO] Total running time: 0h3m51s