[2024-01-24 15:27:41,300] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,302] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fbbf6d5-72fb-4274-8e34-9d9445100455/GCF_005864065.1_ASM586406v1_genomic.fna.gz | prodigal -d GCF_005864065.1_ASM586406v1_genomic.fna/cds.fna -a GCF_005864065.1_ASM586406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:28:05,952] [INFO] Task succeeded: Prodigal
[2024-01-24 15:28:05,953] [INFO] Task started: HMMsearch
[2024-01-24 15:28:05,953] [INFO] Running command: hmmsearch --tblout GCF_005864065.1_ASM586406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference/reference_markers.hmm GCF_005864065.1_ASM586406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:28:06,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:28:06,325] [INFO] Found 6/6 markers.
[2024-01-24 15:28:06,387] [INFO] Query marker FASTA was written to GCF_005864065.1_ASM586406v1_genomic.fna/markers.fasta
[2024-01-24 15:28:06,388] [INFO] Task started: Blastn
[2024-01-24 15:28:06,388] [INFO] Running command: blastn -query GCF_005864065.1_ASM586406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference/reference_markers.fasta -out GCF_005864065.1_ASM586406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:07,697] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:07,701] [INFO] Selected 14 target genomes.
[2024-01-24 15:28:07,701] [INFO] Target genome list was writen to GCF_005864065.1_ASM586406v1_genomic.fna/target_genomes.txt
[2024-01-24 15:28:07,708] [INFO] Task started: fastANI
[2024-01-24 15:28:07,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbbf6d5-72fb-4274-8e34-9d9445100455/GCF_005864065.1_ASM586406v1_genomic.fna.gz --refList GCF_005864065.1_ASM586406v1_genomic.fna/target_genomes.txt --output GCF_005864065.1_ASM586406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:37,452] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:37,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:37,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:37,469] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:37,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:37,469] [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
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	100.0	2685	2690	95	conclusive
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	94.4514	2253	2690	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	94.4016	2197	2690	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	88.3159	1934	2690	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	88.1864	1908	2690	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	88.1185	1975	2690	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	87.7306	1893	2690	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	87.706	1904	2690	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	86.9055	1617	2690	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.1956	1484	2690	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.0924	1117	2690	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.9051	827	2690	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.8588	1316	2690	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.4954	1255	2690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:37,471] [INFO] DFAST Taxonomy check result was written to GCF_005864065.1_ASM586406v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:37,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:37,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:37,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference/checkm_data
[2024-01-24 15:28:37,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:37,560] [INFO] Task started: CheckM
[2024-01-24 15:28:37,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005864065.1_ASM586406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005864065.1_ASM586406v1_genomic.fna/checkm_input GCF_005864065.1_ASM586406v1_genomic.fna/checkm_result
[2024-01-24 15:29:51,409] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:51,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:51,433] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:51,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:51,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005864065.1_ASM586406v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:51,434] [INFO] Task started: Blastn
[2024-01-24 15:29:51,435] [INFO] Running command: blastn -query GCF_005864065.1_ASM586406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d178cd2-47e0-40c3-b7b7-79a397919799/dqc_reference/reference_markers_gtdb.fasta -out GCF_005864065.1_ASM586406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:53,455] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:53,461] [INFO] Selected 8 target genomes.
[2024-01-24 15:29:53,461] [INFO] Target genome list was writen to GCF_005864065.1_ASM586406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:53,468] [INFO] Task started: fastANI
[2024-01-24 15:29:53,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbbf6d5-72fb-4274-8e34-9d9445100455/GCF_005864065.1_ASM586406v1_genomic.fna.gz --refList GCF_005864065.1_ASM586406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005864065.1_ASM586406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:11,806] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:11,816] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:11,816] [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_003260025.2	s__Microbispora triticiradicis	99.1315	2411	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	conclusive
GCF_016863015.1	s__Microbispora amethystogenes	94.3936	2198	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_006334915.2	s__Microbispora catharanthi	88.2976	1938	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_016863095.1	s__Microbispora siamensis	88.2189	1903	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_014161445.1	s__Microbispora sp014161445	87.807	1940	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_900156315.1	s__Microbispora rosea	87.6694	1911	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_012999535.1	s__Microbispora sp012999535	87.07	1767	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647835.1	s__Microbispora aerata	86.9614	1615	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:11,818] [INFO] GTDB search result was written to GCF_005864065.1_ASM586406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:11,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:11,822] [INFO] DFAST_QC result json was written to GCF_005864065.1_ASM586406v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:11,822] [INFO] DFAST_QC completed!
[2024-01-24 15:30:11,822] [INFO] Total running time: 0h2m31s