[2024-01-24 13:18:33,635] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,637] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference
[2024-01-24 13:18:34,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,950] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg59904182-1765-4f3e-ab0f-2d7a31db53aa/GCF_009796285.1_ASM979628v1_genomic.fna.gz | prodigal -d GCF_009796285.1_ASM979628v1_genomic.fna/cds.fna -a GCF_009796285.1_ASM979628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:04,000] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:04,000] [INFO] Task started: HMMsearch
[2024-01-24 13:19:04,000] [INFO] Running command: hmmsearch --tblout GCF_009796285.1_ASM979628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference/reference_markers.hmm GCF_009796285.1_ASM979628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:04,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:04,422] [INFO] Found 6/6 markers.
[2024-01-24 13:19:04,500] [INFO] Query marker FASTA was written to GCF_009796285.1_ASM979628v1_genomic.fna/markers.fasta
[2024-01-24 13:19:04,501] [INFO] Task started: Blastn
[2024-01-24 13:19:04,501] [INFO] Running command: blastn -query GCF_009796285.1_ASM979628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference/reference_markers.fasta -out GCF_009796285.1_ASM979628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:05,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:05,909] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:05,910] [INFO] Target genome list was writen to GCF_009796285.1_ASM979628v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:05,923] [INFO] Task started: fastANI
[2024-01-24 13:19:05,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg59904182-1765-4f3e-ab0f-2d7a31db53aa/GCF_009796285.1_ASM979628v1_genomic.fna.gz --refList GCF_009796285.1_ASM979628v1_genomic.fna/target_genomes.txt --output GCF_009796285.1_ASM979628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:49,024] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:49,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:49,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:49,044] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:49,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:49,044] [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 broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	100.0	3243	3245	95	conclusive
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	90.0573	2276	3245	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	89.0497	2232	3245	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	88.9947	2191	3245	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.9222	2157	3245	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	88.6234	2141	3245	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	88.5141	2136	3245	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	88.4728	2139	3245	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	87.5429	2043	3245	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	87.4864	2042	3245	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	87.448	2067	3245	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	87.3532	1974	3245	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	87.2125	2153	3245	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	87.2036	2141	3245	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.1532	1410	3245	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.7106	1959	3245	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.357	1856	3245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,045] [INFO] DFAST Taxonomy check result was written to GCF_009796285.1_ASM979628v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:49,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:49,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:49,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference/checkm_data
[2024-01-24 13:19:49,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:49,133] [INFO] Task started: CheckM
[2024-01-24 13:19:49,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009796285.1_ASM979628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009796285.1_ASM979628v1_genomic.fna/checkm_input GCF_009796285.1_ASM979628v1_genomic.fna/checkm_result
[2024-01-24 13:22:43,079] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:43,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:22:43,110] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:43,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:43,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009796285.1_ASM979628v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:43,112] [INFO] Task started: Blastn
[2024-01-24 13:22:43,112] [INFO] Running command: blastn -query GCF_009796285.1_ASM979628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd630f25-9bfc-4c7e-a98a-10de3ee83830/dqc_reference/reference_markers_gtdb.fasta -out GCF_009796285.1_ASM979628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:45,551] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:45,555] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:45,555] [INFO] Target genome list was writen to GCF_009796285.1_ASM979628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:45,584] [INFO] Task started: fastANI
[2024-01-24 13:22:45,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg59904182-1765-4f3e-ab0f-2d7a31db53aa/GCF_009796285.1_ASM979628v1_genomic.fna.gz --refList GCF_009796285.1_ASM979628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009796285.1_ASM979628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:24,638] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:24,656] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:24,656] [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_009796285.1	s__Streptomyces broussonetiae	100.0	3241	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001636945.1	s__Streptomyces sp001636945	91.999	2313	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	90.2856	2295	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	90.0627	2274	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_001514035.1	s__Streptomyces yokosukanensis	89.0332	2236	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	89.0036	2190	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953885.1	s__Streptomyces sp001953885	88.9176	2238	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650595.1	s__Streptomyces alanosinicus	88.626	2142	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649495.1	s__Streptomyces filipinensis	88.4622	2140	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_000716535.1	s__Streptomyces flaveolus_A	87.5596	2045	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCA_014649295.1	s__Streptomyces libani_A	87.3086	1871	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009865385.1	s__Streptomyces sp009865385	87.2094	1723	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542625.1	s__Streptomyces griseochromogenes	87.2031	2156	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003634225.1	s__Streptomyces sp003634225	87.0811	2168	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.82	0.97	0.97	3	-
GCA_016432725.1	s__Streptomyces sp016432725	86.6241	1838	3245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,658] [INFO] GTDB search result was written to GCF_009796285.1_ASM979628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:24,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:24,663] [INFO] DFAST_QC result json was written to GCF_009796285.1_ASM979628v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:24,663] [INFO] DFAST_QC completed!
[2024-01-24 13:23:24,663] [INFO] Total running time: 0h4m51s