[2024-01-24 15:14:49,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:49,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:49,423] [INFO] DQC Reference Directory: /var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference
[2024-01-24 15:14:50,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:50,690] [INFO] Task started: Prodigal
[2024-01-24 15:14:50,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fa32f99-dd08-4bfe-980c-309234d9af29/GCF_014204985.1_ASM1420498v1_genomic.fna.gz | prodigal -d GCF_014204985.1_ASM1420498v1_genomic.fna/cds.fna -a GCF_014204985.1_ASM1420498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:13,858] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:13,859] [INFO] Task started: HMMsearch
[2024-01-24 15:15:13,859] [INFO] Running command: hmmsearch --tblout GCF_014204985.1_ASM1420498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference/reference_markers.hmm GCF_014204985.1_ASM1420498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:14,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:14,205] [INFO] Found 6/6 markers.
[2024-01-24 15:15:14,269] [INFO] Query marker FASTA was written to GCF_014204985.1_ASM1420498v1_genomic.fna/markers.fasta
[2024-01-24 15:15:14,270] [INFO] Task started: Blastn
[2024-01-24 15:15:14,270] [INFO] Running command: blastn -query GCF_014204985.1_ASM1420498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference/reference_markers.fasta -out GCF_014204985.1_ASM1420498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:15,646] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:15,650] [INFO] Selected 18 target genomes.
[2024-01-24 15:15:15,651] [INFO] Target genome list was writen to GCF_014204985.1_ASM1420498v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:15,658] [INFO] Task started: fastANI
[2024-01-24 15:15:15,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fa32f99-dd08-4bfe-980c-309234d9af29/GCF_014204985.1_ASM1420498v1_genomic.fna.gz --refList GCF_014204985.1_ASM1420498v1_genomic.fna/target_genomes.txt --output GCF_014204985.1_ASM1420498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:52,304] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:52,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:52,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:52,320] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:15:52,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:52,320] [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
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	100.0	2606	2607	95	conclusive
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	99.9887	2565	2607	95	conclusive
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	85.019	1637	2607	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	84.7347	1755	2607	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.6445	1661	2607	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	84.6406	1586	2607	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.6303	1467	2607	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.5085	1510	2607	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	83.4854	1531	2607	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	83.3867	1526	2607	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	83.2578	1516	2607	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	83.2268	1502	2607	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	83.1125	1544	2607	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.3883	1368	2607	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.2451	906	2607	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.9048	1276	2607	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	79.8591	1266	2607	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.5535	1295	2607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:52,322] [INFO] DFAST Taxonomy check result was written to GCF_014204985.1_ASM1420498v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:52,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:52,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:52,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference/checkm_data
[2024-01-24 15:15:52,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:52,396] [INFO] Task started: CheckM
[2024-01-24 15:15:52,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204985.1_ASM1420498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204985.1_ASM1420498v1_genomic.fna/checkm_input GCF_014204985.1_ASM1420498v1_genomic.fna/checkm_result
[2024-01-24 15:17:23,521] [INFO] Task succeeded: CheckM
[2024-01-24 15:17:23,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:17:23,546] [INFO] ===== Completeness check finished =====
[2024-01-24 15:17:23,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:17:23,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204985.1_ASM1420498v1_genomic.fna/markers.fasta)
[2024-01-24 15:17:23,548] [INFO] Task started: Blastn
[2024-01-24 15:17:23,548] [INFO] Running command: blastn -query GCF_014204985.1_ASM1420498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b4435c-19eb-4569-8cb6-e6e9b35aa41d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204985.1_ASM1420498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:17:25,750] [INFO] Task succeeded: Blastn
[2024-01-24 15:17:25,763] [INFO] Selected 20 target genomes.
[2024-01-24 15:17:25,763] [INFO] Target genome list was writen to GCF_014204985.1_ASM1420498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:17:25,777] [INFO] Task started: fastANI
[2024-01-24 15:17:25,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fa32f99-dd08-4bfe-980c-309234d9af29/GCF_014204985.1_ASM1420498v1_genomic.fna.gz --refList GCF_014204985.1_ASM1420498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204985.1_ASM1420498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:18:00,412] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:00,429] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:18:00,430] [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_014204985.1	s__Streptosporangium becharense	100.0	2606	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000721075.1	s__Streptosporangium amethystogenes	85.0334	1635	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	84.6969	1755	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149035.1	s__Streptosporangium minutum	84.6433	1585	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	84.6153	1666	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_900188345.1	s__Streptosporangium subroseum	84.0266	1605	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	83.6248	1533	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409935.1	s__Streptosporangium sandarakinum	83.6188	1469	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	83.617	1546	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.5665	1502	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	83.4995	1529	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	83.4149	1506	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_016863195.1	s__Planobispora takensis	83.4081	1522	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	83.2137	1524	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863135.1	s__Planobispora longispora	83.0734	1549	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203715.1	s__Streptosporangium saharense	82.5915	1422	2607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778045.1	s__UBA2862 sp902778045	74.6916	65	2607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785105.1	s__UBA2862 sp902785105	74.6028	67	2607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:18:00,432] [INFO] GTDB search result was written to GCF_014204985.1_ASM1420498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:18:00,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:18:00,436] [INFO] DFAST_QC result json was written to GCF_014204985.1_ASM1420498v1_genomic.fna/dqc_result.json
[2024-01-24 15:18:00,436] [INFO] DFAST_QC completed!
[2024-01-24 15:18:00,436] [INFO] Total running time: 0h3m11s