[2024-01-24 11:13:49,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,586] [INFO] DQC Reference Directory: /var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference
[2024-01-24 11:13:50,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,808] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,808] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0c88ad6-5123-40b9-8bde-e107add025d7/GCF_014650135.1_ASM1465013v1_genomic.fna.gz | prodigal -d GCF_014650135.1_ASM1465013v1_genomic.fna/cds.fna -a GCF_014650135.1_ASM1465013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:16,011] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:16,012] [INFO] Task started: HMMsearch
[2024-01-24 11:14:16,012] [INFO] Running command: hmmsearch --tblout GCF_014650135.1_ASM1465013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference/reference_markers.hmm GCF_014650135.1_ASM1465013v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:16,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:16,367] [INFO] Found 6/6 markers.
[2024-01-24 11:14:16,429] [INFO] Query marker FASTA was written to GCF_014650135.1_ASM1465013v1_genomic.fna/markers.fasta
[2024-01-24 11:14:16,429] [INFO] Task started: Blastn
[2024-01-24 11:14:16,430] [INFO] Running command: blastn -query GCF_014650135.1_ASM1465013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference/reference_markers.fasta -out GCF_014650135.1_ASM1465013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:17,724] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:17,728] [INFO] Selected 20 target genomes.
[2024-01-24 11:14:17,729] [INFO] Target genome list was writen to GCF_014650135.1_ASM1465013v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:17,742] [INFO] Task started: fastANI
[2024-01-24 11:14:17,743] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0c88ad6-5123-40b9-8bde-e107add025d7/GCF_014650135.1_ASM1465013v1_genomic.fna.gz --refList GCF_014650135.1_ASM1465013v1_genomic.fna/target_genomes.txt --output GCF_014650135.1_ASM1465013v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:59,304] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:59,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:59,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:59,324] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:14:59,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:14:59,324] [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 mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	92.0088	1979	2707	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	89.8571	2087	2707	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	89.605	1988	2707	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	89.6012	2029	2707	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	89.5745	2034	2707	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	89.573	1961	2707	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	89.2046	1915	2707	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	89.1794	1947	2707	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	89.1626	1898	2707	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	89.0519	1913	2707	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_015645455.1	47716	47716	type	True	88.724	1855	2707	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	88.6426	1892	2707	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	88.2732	1918	2707	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.496	1560	2707	95	below_threshold
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	86.4548	1724	2707	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	86.4204	1776	2707	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.8262	1801	2707	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.5768	1602	2707	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	85.402	1629	2707	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.1385	1528	2707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:59,326] [INFO] DFAST Taxonomy check result was written to GCF_014650135.1_ASM1465013v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:59,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:59,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:59,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference/checkm_data
[2024-01-24 11:14:59,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:59,408] [INFO] Task started: CheckM
[2024-01-24 11:14:59,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650135.1_ASM1465013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650135.1_ASM1465013v1_genomic.fna/checkm_input GCF_014650135.1_ASM1465013v1_genomic.fna/checkm_result
[2024-01-24 11:17:01,104] [INFO] Task succeeded: CheckM
[2024-01-24 11:17:01,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:17:01,134] [INFO] ===== Completeness check finished =====
[2024-01-24 11:17:01,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:17:01,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650135.1_ASM1465013v1_genomic.fna/markers.fasta)
[2024-01-24 11:17:01,135] [INFO] Task started: Blastn
[2024-01-24 11:17:01,135] [INFO] Running command: blastn -query GCF_014650135.1_ASM1465013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd399f39d-627a-47af-8b51-50b67f384e99/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650135.1_ASM1465013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:17:03,192] [INFO] Task succeeded: Blastn
[2024-01-24 11:17:03,196] [INFO] Selected 15 target genomes.
[2024-01-24 11:17:03,196] [INFO] Target genome list was writen to GCF_014650135.1_ASM1465013v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:17:03,248] [INFO] Task started: fastANI
[2024-01-24 11:17:03,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0c88ad6-5123-40b9-8bde-e107add025d7/GCF_014650135.1_ASM1465013v1_genomic.fna.gz --refList GCF_014650135.1_ASM1465013v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650135.1_ASM1465013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:17:35,322] [INFO] Task succeeded: fastANI
[2024-01-24 11:17:35,340] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:17:35,340] [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_002155895.1	s__Streptomyces rochei	98.6206	2026	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	conclusive
GCF_001905385.1	s__Streptomyces sp001905385	92.5667	2064	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_014649815.1	s__Streptomyces mutabilis	91.9835	1982	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.69	95.91	0.82	0.76	4	-
GCF_002005225.1	s__Streptomyces pactum_A	90.0909	2029	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001267885.1	s__Streptomyces ambofaciens	89.8401	2091	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_000772045.1	s__Streptomyces sp000772045	89.7747	2041	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_002939385.1	s__Streptomyces sp002939385	89.6803	1894	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_000717995.1	s__Streptomyces violaceorubidus	89.6096	1866	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112595.1	s__Streptomyces rubrogriseus	89.5873	2032	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	89.3932	2055	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_003112575.1	s__Streptomyces ardesiacus	89.2035	1941	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_002005565.1	s__Streptomyces sp002005565	89.1399	1796	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648855.1	s__Streptomyces parvulus	89.033	1916	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_018982965.1	s__Streptomyces sp018982965	88.8192	1802	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614415.1	s__Streptomyces sp018614415	86.8186	1695	2707	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 11:17:35,342] [INFO] GTDB search result was written to GCF_014650135.1_ASM1465013v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:17:35,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:17:35,346] [INFO] DFAST_QC result json was written to GCF_014650135.1_ASM1465013v1_genomic.fna/dqc_result.json
[2024-01-24 11:17:35,346] [INFO] DFAST_QC completed!
[2024-01-24 11:17:35,346] [INFO] Total running time: 0h3m46s