[2024-01-25 18:48:05,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:05,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:05,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference
[2024-01-25 18:48:06,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:06,739] [INFO] Task started: Prodigal
[2024-01-25 18:48:06,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bb1f1b4-8c09-4604-a112-08eaf1dcc0b9/GCF_000718175.1_ASM71817v1_genomic.fna.gz | prodigal -d GCF_000718175.1_ASM71817v1_genomic.fna/cds.fna -a GCF_000718175.1_ASM71817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:27,407] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:27,407] [INFO] Task started: HMMsearch
[2024-01-25 18:48:27,407] [INFO] Running command: hmmsearch --tblout GCF_000718175.1_ASM71817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference/reference_markers.hmm GCF_000718175.1_ASM71817v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:27,715] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:27,716] [INFO] Found 6/6 markers.
[2024-01-25 18:48:27,781] [INFO] Query marker FASTA was written to GCF_000718175.1_ASM71817v1_genomic.fna/markers.fasta
[2024-01-25 18:48:27,782] [INFO] Task started: Blastn
[2024-01-25 18:48:27,782] [INFO] Running command: blastn -query GCF_000718175.1_ASM71817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference/reference_markers.fasta -out GCF_000718175.1_ASM71817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:29,025] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:29,028] [INFO] Selected 15 target genomes.
[2024-01-25 18:48:29,028] [INFO] Target genome list was writen to GCF_000718175.1_ASM71817v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:29,033] [INFO] Task started: fastANI
[2024-01-25 18:48:29,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb1f1b4-8c09-4604-a112-08eaf1dcc0b9/GCF_000718175.1_ASM71817v1_genomic.fna.gz --refList GCF_000718175.1_ASM71817v1_genomic.fna/target_genomes.txt --output GCF_000718175.1_ASM71817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:02,160] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:02,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:02,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:02,170] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:49:02,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:02,170] [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 exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	100.0	2588	2594	95	conclusive
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	99.9873	2565	2594	95	conclusive
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	90.4331	1932	2594	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_000253235.1	54571	54571	type	True	90.2381	1946	2594	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_008639165.1	54571	54571	type	True	90.201	1946	2594	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	90.0406	1501	2594	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.7161	1960	2594	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.6382	1960	2594	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	89.4653	1957	2594	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	89.4307	1998	2594	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.3231	1944	2594	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	89.3146	1948	2594	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	81.6027	1413	2594	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.481	1354	2594	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.3714	1228	2594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:02,171] [INFO] DFAST Taxonomy check result was written to GCF_000718175.1_ASM71817v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:02,172] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:02,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:02,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference/checkm_data
[2024-01-25 18:49:02,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:02,253] [INFO] Task started: CheckM
[2024-01-25 18:49:02,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718175.1_ASM71817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718175.1_ASM71817v1_genomic.fna/checkm_input GCF_000718175.1_ASM71817v1_genomic.fna/checkm_result
[2024-01-25 18:50:44,354] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:44,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 14.06%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:44,382] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:44,382] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:44,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718175.1_ASM71817v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:44,383] [INFO] Task started: Blastn
[2024-01-25 18:50:44,383] [INFO] Running command: blastn -query GCF_000718175.1_ASM71817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc357fcdd-1f7f-4ac5-9fcd-9463c63e98b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718175.1_ASM71817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:46,551] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:46,554] [INFO] Selected 13 target genomes.
[2024-01-25 18:50:46,554] [INFO] Target genome list was writen to GCF_000718175.1_ASM71817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:46,566] [INFO] Task started: fastANI
[2024-01-25 18:50:46,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb1f1b4-8c09-4604-a112-08eaf1dcc0b9/GCF_000718175.1_ASM71817v1_genomic.fna.gz --refList GCF_000718175.1_ASM71817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718175.1_ASM71817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:15,013] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:15,022] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:15,022] [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_000725545.1	s__Streptomyces exfoliatus	99.9873	2565	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	conclusive
GCA_000717735.1	s__Streptomyces griseoluteus_A	96.271	2210	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_001905665.1	s__Streptomyces sp001905665	90.7601	1996	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656215.1	s__Streptomyces zaomyceticus	90.4188	1934	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008639165.1	s__Streptomyces venezuelae	90.1848	1948	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCF_001418135.1	s__Streptomyces aureus_A	90.1789	1723	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	90.1224	1903	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905825.1	s__Streptomyces sp001905825	89.8769	1986	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_014451325.1	s__Streptomyces sp014451325	89.7963	1383	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.6907	1963	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_006539185.1	s__Streptomyces gardneri	89.4716	1957	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_003386135.1	s__Streptomyces sp003386135	89.3714	1928	2594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_008042145.1	s__Streptomyces sp008042145	89.364	1797	2594	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 18:51:15,024] [INFO] GTDB search result was written to GCF_000718175.1_ASM71817v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:15,024] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:15,027] [INFO] DFAST_QC result json was written to GCF_000718175.1_ASM71817v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:15,028] [INFO] DFAST_QC completed!
[2024-01-25 18:51:15,028] [INFO] Total running time: 0h3m9s