[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbe5e4b4-a248-41e4-9166-36d65b325fef/GCF_008632535.1_ASM863253v1_genomic.fna.gz | prodigal -d GCF_008632535.1_ASM863253v1_genomic.fna/cds.fna -a GCF_008632535.1_ASM863253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:31,869] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:31,870] [INFO] Task started: HMMsearch
[2024-01-24 10:47:31,870] [INFO] Running command: hmmsearch --tblout GCF_008632535.1_ASM863253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference/reference_markers.hmm GCF_008632535.1_ASM863253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:32,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:32,210] [INFO] Found 6/6 markers.
[2024-01-24 10:47:32,268] [INFO] Query marker FASTA was written to GCF_008632535.1_ASM863253v1_genomic.fna/markers.fasta
[2024-01-24 10:47:32,269] [INFO] Task started: Blastn
[2024-01-24 10:47:32,269] [INFO] Running command: blastn -query GCF_008632535.1_ASM863253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference/reference_markers.fasta -out GCF_008632535.1_ASM863253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:33,571] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:33,574] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:33,575] [INFO] Target genome list was writen to GCF_008632535.1_ASM863253v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:33,581] [INFO] Task started: fastANI
[2024-01-24 10:47:33,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe5e4b4-a248-41e4-9166-36d65b325fef/GCF_008632535.1_ASM863253v1_genomic.fna.gz --refList GCF_008632535.1_ASM863253v1_genomic.fna/target_genomes.txt --output GCF_008632535.1_ASM863253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:58,396] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:58,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:58,408] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:58,408] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:58,408] [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 parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	100.0	2381	2396	95	inconclusive
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	99.9634	2384	2396	95	inconclusive
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	95.0029	1941	2396	95	inconclusive
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	94.5461	1921	2396	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	92.0826	1901	2396	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	91.4183	1932	2396	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.4895	1834	2396	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	89.0101	1488	2396	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.5868	1496	2396	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	81.4173	1275	2396	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.3632	1221	2396	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.2531	1130	2396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,410] [INFO] DFAST Taxonomy check result was written to GCF_008632535.1_ASM863253v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:58,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:58,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:58,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference/checkm_data
[2024-01-24 10:47:58,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:58,487] [INFO] Task started: CheckM
[2024-01-24 10:47:58,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008632535.1_ASM863253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008632535.1_ASM863253v1_genomic.fna/checkm_input GCF_008632535.1_ASM863253v1_genomic.fna/checkm_result
[2024-01-24 10:49:03,034] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:03,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:03,064] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:03,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:03,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008632535.1_ASM863253v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:03,065] [INFO] Task started: Blastn
[2024-01-24 10:49:03,065] [INFO] Running command: blastn -query GCF_008632535.1_ASM863253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeece5afd-49d9-4153-9df4-b33f757ee53b/dqc_reference/reference_markers_gtdb.fasta -out GCF_008632535.1_ASM863253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:05,089] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:05,092] [INFO] Selected 9 target genomes.
[2024-01-24 10:49:05,093] [INFO] Target genome list was writen to GCF_008632535.1_ASM863253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:05,099] [INFO] Task started: fastANI
[2024-01-24 10:49:05,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe5e4b4-a248-41e4-9166-36d65b325fef/GCF_008632535.1_ASM863253v1_genomic.fna.gz --refList GCF_008632535.1_ASM863253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008632535.1_ASM863253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:23,008] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:23,017] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:23,017] [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_014648875.1	s__Streptomyces parvus	99.9634	2384	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	conclusive
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	95.1202	1953	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_014649035.1	s__Streptomyces sindenensis	94.9924	1942	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	-
GCA_014649555.1	s__Streptomyces globisporus	94.8552	1953	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_003501885.1	s__Streptomyces globisporus_D	94.784	1798	2396	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	94.7464	1937	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718455.1	s__Streptomyces globisporus_A	94.3859	1823	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_018866325.1	s__Streptomyces sp001895105	93.3322	1878	2396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
GCA_002551355.1	s__Streptomyces sp002551355	93.0165	1907	2396	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 10:49:23,018] [INFO] GTDB search result was written to GCF_008632535.1_ASM863253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:23,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:23,022] [INFO] DFAST_QC result json was written to GCF_008632535.1_ASM863253v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:23,022] [INFO] DFAST_QC completed!
[2024-01-24 10:49:23,022] [INFO] Total running time: 0h2m16s