[2024-01-24 13:55:46,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:46,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:46,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference
[2024-01-24 13:55:48,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:48,242] [INFO] Task started: Prodigal
[2024-01-24 13:55:48,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg365d0e57-d44e-4c7d-84f2-428ea76be535/GCF_014650715.1_ASM1465071v1_genomic.fna.gz | prodigal -d GCF_014650715.1_ASM1465071v1_genomic.fna/cds.fna -a GCF_014650715.1_ASM1465071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:26,234] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:26,235] [INFO] Task started: HMMsearch
[2024-01-24 13:56:26,235] [INFO] Running command: hmmsearch --tblout GCF_014650715.1_ASM1465071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference/reference_markers.hmm GCF_014650715.1_ASM1465071v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:26,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:26,583] [INFO] Found 6/6 markers.
[2024-01-24 13:56:26,650] [INFO] Query marker FASTA was written to GCF_014650715.1_ASM1465071v1_genomic.fna/markers.fasta
[2024-01-24 13:56:26,651] [INFO] Task started: Blastn
[2024-01-24 13:56:26,651] [INFO] Running command: blastn -query GCF_014650715.1_ASM1465071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference/reference_markers.fasta -out GCF_014650715.1_ASM1465071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:27,980] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:27,985] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:27,985] [INFO] Target genome list was writen to GCF_014650715.1_ASM1465071v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:28,004] [INFO] Task started: fastANI
[2024-01-24 13:56:28,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg365d0e57-d44e-4c7d-84f2-428ea76be535/GCF_014650715.1_ASM1465071v1_genomic.fna.gz --refList GCF_014650715.1_ASM1465071v1_genomic.fna/target_genomes.txt --output GCF_014650715.1_ASM1465071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:09,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:09,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:09,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:09,430] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:09,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:09,430] [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 bluensis	strain=JCM 4729	GCA_014650715.1	33897	33897	type	True	100.0	2979	2984	95	conclusive
Streptomyces acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	93.6362	2206	2984	95	below_threshold
Streptomyces spongiae	strain=NBRC 106415	GCA_009377185.1	565072	565072	type	True	89.9868	1819	2984	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	88.0339	1688	2984	95	below_threshold
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	85.5616	1718	2984	95	below_threshold
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	85.2967	1628	2984	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	85.0182	1793	2984	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	84.8018	1839	2984	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	84.7237	1522	2984	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	84.709	1877	2984	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.6787	1892	2984	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	84.509	1808	2984	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.3693	1632	2984	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.2932	1825	2984	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	84.0689	1474	2984	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.0322	1620	2984	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	83.7653	1388	2984	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	83.7295	1517	2984	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	83.5732	1548	2984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:09,432] [INFO] DFAST Taxonomy check result was written to GCF_014650715.1_ASM1465071v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:09,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:09,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:09,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference/checkm_data
[2024-01-24 13:57:09,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:09,515] [INFO] Task started: CheckM
[2024-01-24 13:57:09,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650715.1_ASM1465071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650715.1_ASM1465071v1_genomic.fna/checkm_input GCF_014650715.1_ASM1465071v1_genomic.fna/checkm_result
[2024-01-24 13:59:18,838] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:18,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:18,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:18,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:18,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650715.1_ASM1465071v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:18,867] [INFO] Task started: Blastn
[2024-01-24 13:59:18,867] [INFO] Running command: blastn -query GCF_014650715.1_ASM1465071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ccd82f-f1eb-431d-9e4e-6dd3a1ceaba9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650715.1_ASM1465071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:20,930] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:20,936] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:20,936] [INFO] Target genome list was writen to GCF_014650715.1_ASM1465071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:20,956] [INFO] Task started: fastANI
[2024-01-24 13:59:20,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg365d0e57-d44e-4c7d-84f2-428ea76be535/GCF_014650715.1_ASM1465071v1_genomic.fna.gz --refList GCF_014650715.1_ASM1465071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650715.1_ASM1465071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:05,046] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:05,062] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:05,063] [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_014650715.1	s__Streptomyces bluensis	100.0	2979	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.08	99.08	0.92	0.92	2	conclusive
GCF_009377235.1	s__Streptomyces acidicola	93.6289	2208	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.86	96.86	0.86	0.86	2	-
GCF_009377205.1	s__Streptomyces phyllanthi	88.0096	1691	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650915.1	s__Streptomyces poonensis	85.5334	1724	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648075.1	s__Streptomyces ruber	85.304	1628	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386495.1	s__Streptomyces tailanensis	84.9986	1795	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214185.1	s__Streptomyces capitiformicae	84.715	1878	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	-
GCF_001418645.1	s__Streptomyces neyagawaensis	84.6703	1363	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_900290235.1	s__Streptomyces sp900290235	84.6452	1837	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	96.28	96.28	0.86	0.86	2	-
GCF_000719285.1	s__Streptomyces bicolor	84.3961	1759	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	84.2911	1825	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.2292	1840	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	84.1281	1648	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	83.9968	1628	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	83.9838	1662	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091315.1	s__Streptomyces sp900091315	83.7086	1610	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	83.6919	1568	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	83.5952	1549	2984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	83.5573	1550	2984	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 14:00:05,064] [INFO] GTDB search result was written to GCF_014650715.1_ASM1465071v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:05,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:05,072] [INFO] DFAST_QC result json was written to GCF_014650715.1_ASM1465071v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:05,072] [INFO] DFAST_QC completed!
[2024-01-24 14:00:05,072] [INFO] Total running time: 0h4m18s