[2024-01-24 15:17:48,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:48,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:48,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,535] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b99c6d3-9483-43c7-8407-9a42df6e2966/GCF_014203605.1_ASM1420360v1_genomic.fna.gz | prodigal -d GCF_014203605.1_ASM1420360v1_genomic.fna/cds.fna -a GCF_014203605.1_ASM1420360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:12,425] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:12,426] [INFO] Task started: HMMsearch
[2024-01-24 15:18:12,426] [INFO] Running command: hmmsearch --tblout GCF_014203605.1_ASM1420360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference/reference_markers.hmm GCF_014203605.1_ASM1420360v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:12,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:12,778] [INFO] Found 6/6 markers.
[2024-01-24 15:18:12,843] [INFO] Query marker FASTA was written to GCF_014203605.1_ASM1420360v1_genomic.fna/markers.fasta
[2024-01-24 15:18:12,843] [INFO] Task started: Blastn
[2024-01-24 15:18:12,843] [INFO] Running command: blastn -query GCF_014203605.1_ASM1420360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference/reference_markers.fasta -out GCF_014203605.1_ASM1420360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:14,242] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:14,247] [INFO] Selected 23 target genomes.
[2024-01-24 15:18:14,248] [INFO] Target genome list was writen to GCF_014203605.1_ASM1420360v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:14,263] [INFO] Task started: fastANI
[2024-01-24 15:18:14,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b99c6d3-9483-43c7-8407-9a42df6e2966/GCF_014203605.1_ASM1420360v1_genomic.fna.gz --refList GCF_014203605.1_ASM1420360v1_genomic.fna/target_genomes.txt --output GCF_014203605.1_ASM1420360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:06,115] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:06,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:06,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:06,133] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:06,133] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:06,133] [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
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	88.8839	2081	2684	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	88.5485	2001	2684	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	88.4752	2029	2684	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	87.9346	2024	2684	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	87.8982	2036	2684	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	86.9891	1791	2684	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	86.9524	1773	2684	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	86.7638	1840	2684	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	84.9187	1772	2684	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.8701	1698	2684	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.6841	1540	2684	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.6379	1586	2684	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	80.9292	1437	2684	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.7396	1455	2684	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.7389	989	2684	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	80.7387	1471	2684	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	80.6216	1396	2684	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.4615	1451	2684	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.4129	1429	2684	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	80.2624	1483	2684	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	79.7212	1113	2684	95	below_threshold
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	79.4165	1145	2684	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	77.6768	1012	2684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,135] [INFO] DFAST Taxonomy check result was written to GCF_014203605.1_ASM1420360v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:06,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:06,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:06,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference/checkm_data
[2024-01-24 15:19:06,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:06,211] [INFO] Task started: CheckM
[2024-01-24 15:19:06,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203605.1_ASM1420360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203605.1_ASM1420360v1_genomic.fna/checkm_input GCF_014203605.1_ASM1420360v1_genomic.fna/checkm_result
[2024-01-24 15:20:38,483] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:38,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:38,517] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:38,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:38,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203605.1_ASM1420360v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:38,519] [INFO] Task started: Blastn
[2024-01-24 15:20:38,519] [INFO] Running command: blastn -query GCF_014203605.1_ASM1420360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd13d07d0-d2a3-44b1-9e3a-8a0556b34c30/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203605.1_ASM1420360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:40,721] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:40,725] [INFO] Selected 15 target genomes.
[2024-01-24 15:20:40,725] [INFO] Target genome list was writen to GCF_014203605.1_ASM1420360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:40,740] [INFO] Task started: fastANI
[2024-01-24 15:20:40,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b99c6d3-9483-43c7-8407-9a42df6e2966/GCF_014203605.1_ASM1420360v1_genomic.fna.gz --refList GCF_014203605.1_ASM1420360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203605.1_ASM1420360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:14,713] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:14,738] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:14,739] [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_014203605.1	s__Planomonospora_A venezuelensis	100.0	2679	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015711605.1	s__Planomonospora_A sp015711605	90.9732	2078	2684	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_016863135.1	s__Planobispora longispora	88.9037	2079	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	88.4626	2030	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863195.1	s__Planobispora takensis	87.9508	2021	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	87.9258	2031	2684	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	86.8535	1805	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_015711645.1	s__Planomonospora sp015711645	86.838	1769	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	84.887	1695	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_013409935.1	s__Streptosporangium sandarakinum	83.6773	1540	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.6277	1588	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	80.6269	1395	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863335.1	s__Planotetraspora thailandica	79.6801	1121	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570545.1	s__Herbidospora mongoliensis	79.3715	1155	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349235.1	s__Spirillospora darangshiensis	77.6816	1010	2684	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:14,741] [INFO] GTDB search result was written to GCF_014203605.1_ASM1420360v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:14,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:14,746] [INFO] DFAST_QC result json was written to GCF_014203605.1_ASM1420360v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:14,746] [INFO] DFAST_QC completed!
[2024-01-24 15:21:14,746] [INFO] Total running time: 0h3m26s