[2024-01-24 14:55:50,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference
[2024-01-24 14:55:52,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,196] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,196] [INFO] Running command: gunzip -c /var/lib/cwl/stg59cd258a-f18e-4e20-9986-bd1b15f874e7/GCF_014205055.1_ASM1420505v1_genomic.fna.gz | prodigal -d GCF_014205055.1_ASM1420505v1_genomic.fna/cds.fna -a GCF_014205055.1_ASM1420505v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:21,392] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:21,393] [INFO] Task started: HMMsearch
[2024-01-24 14:56:21,393] [INFO] Running command: hmmsearch --tblout GCF_014205055.1_ASM1420505v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference/reference_markers.hmm GCF_014205055.1_ASM1420505v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:21,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:21,759] [INFO] Found 6/6 markers.
[2024-01-24 14:56:21,837] [INFO] Query marker FASTA was written to GCF_014205055.1_ASM1420505v1_genomic.fna/markers.fasta
[2024-01-24 14:56:21,838] [INFO] Task started: Blastn
[2024-01-24 14:56:21,838] [INFO] Running command: blastn -query GCF_014205055.1_ASM1420505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference/reference_markers.fasta -out GCF_014205055.1_ASM1420505v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:23,163] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:23,166] [INFO] Selected 18 target genomes.
[2024-01-24 14:56:23,166] [INFO] Target genome list was writen to GCF_014205055.1_ASM1420505v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:23,173] [INFO] Task started: fastANI
[2024-01-24 14:56:23,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg59cd258a-f18e-4e20-9986-bd1b15f874e7/GCF_014205055.1_ASM1420505v1_genomic.fna.gz --refList GCF_014205055.1_ASM1420505v1_genomic.fna/target_genomes.txt --output GCF_014205055.1_ASM1420505v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:04,385] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:04,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:04,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:04,400] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:57:04,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:04,401] [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 luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	100.0	2901	2902	95	conclusive
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	94.8958	2440	2902	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	94.3878	2164	2902	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	92.9798	2383	2902	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	92.7246	2281	2902	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	92.6603	2303	2902	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.4126	2305	2902	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.3919	2306	2902	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	92.1567	1844	2902	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	91.9954	2023	2902	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.843	2186	2902	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.612	2247	2902	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2837	1511	2902	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	84.7576	1678	2902	95	below_threshold
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	84.6637	1646	2902	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.1035	829	2902	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.6485	1027	2902	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.4159	924	2902	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:04,403] [INFO] DFAST Taxonomy check result was written to GCF_014205055.1_ASM1420505v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:04,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:04,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:04,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference/checkm_data
[2024-01-24 14:57:04,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:04,483] [INFO] Task started: CheckM
[2024-01-24 14:57:04,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205055.1_ASM1420505v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205055.1_ASM1420505v1_genomic.fna/checkm_input GCF_014205055.1_ASM1420505v1_genomic.fna/checkm_result
[2024-01-24 14:59:54,015] [INFO] Task succeeded: CheckM
[2024-01-24 14:59:54,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:59:54,043] [INFO] ===== Completeness check finished =====
[2024-01-24 14:59:54,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:59:54,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205055.1_ASM1420505v1_genomic.fna/markers.fasta)
[2024-01-24 14:59:54,045] [INFO] Task started: Blastn
[2024-01-24 14:59:54,045] [INFO] Running command: blastn -query GCF_014205055.1_ASM1420505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1e2d1ea-2eb0-4701-a947-fa9d7b11f52d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205055.1_ASM1420505v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:59:56,233] [INFO] Task succeeded: Blastn
[2024-01-24 14:59:56,237] [INFO] Selected 13 target genomes.
[2024-01-24 14:59:56,237] [INFO] Target genome list was writen to GCF_014205055.1_ASM1420505v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:59:56,250] [INFO] Task started: fastANI
[2024-01-24 14:59:56,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg59cd258a-f18e-4e20-9986-bd1b15f874e7/GCF_014205055.1_ASM1420505v1_genomic.fna.gz --refList GCF_014205055.1_ASM1420505v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205055.1_ASM1420505v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:00:25,693] [INFO] Task succeeded: fastANI
[2024-01-24 15:00:25,706] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:00:25,706] [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_014205055.1	s__Streptomyces luteogriseus	100.0	2899	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	conclusive
GCF_014648995.1	s__Streptomyces massasporeus	94.8931	2441	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCA_014204745.1	s__Streptomyces collinus	92.9583	2361	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_004803895.1	s__Streptomyces hawaiiensis	92.9087	2303	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014202475.1	s__Streptomyces paradoxus	92.8158	2307	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	92.7245	2281	2902	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	92.6614	2343	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_007655005.1	s__Streptomyces tibetensis	92.4202	2304	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001280065.1	s__Streptomyces sp001280065	91.9713	2201	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	85.1806	1782	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCA_014649155.1	s__Streptomyces griseoviridis	84.7204	1660	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.52	99.48	0.96	0.96	3	-
GCF_010548275.1	s__Streptomyces sp010548275	83.9573	1788	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	78.4445	925	2902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:00:25,708] [INFO] GTDB search result was written to GCF_014205055.1_ASM1420505v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:00:25,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:00:25,712] [INFO] DFAST_QC result json was written to GCF_014205055.1_ASM1420505v1_genomic.fna/dqc_result.json
[2024-01-24 15:00:25,712] [INFO] DFAST_QC completed!
[2024-01-24 15:00:25,712] [INFO] Total running time: 0h4m35s