[2024-01-24 11:26:38,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference
[2024-01-24 11:26:39,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,688] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,688] [INFO] Running command: gunzip -c /var/lib/cwl/stga88ceb77-a78c-45ca-ad98-945b746ba859/GCF_016863115.1_ASM1686311v1_genomic.fna.gz | prodigal -d GCF_016863115.1_ASM1686311v1_genomic.fna/cds.fna -a GCF_016863115.1_ASM1686311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:56,617] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:56,617] [INFO] Task started: HMMsearch
[2024-01-24 11:26:56,618] [INFO] Running command: hmmsearch --tblout GCF_016863115.1_ASM1686311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference/reference_markers.hmm GCF_016863115.1_ASM1686311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:56,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:56,935] [INFO] Found 6/6 markers.
[2024-01-24 11:26:56,990] [INFO] Query marker FASTA was written to GCF_016863115.1_ASM1686311v1_genomic.fna/markers.fasta
[2024-01-24 11:26:56,990] [INFO] Task started: Blastn
[2024-01-24 11:26:56,991] [INFO] Running command: blastn -query GCF_016863115.1_ASM1686311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference/reference_markers.fasta -out GCF_016863115.1_ASM1686311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:58,211] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:58,215] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:58,215] [INFO] Target genome list was writen to GCF_016863115.1_ASM1686311v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:58,245] [INFO] Task started: fastANI
[2024-01-24 11:26:58,246] [INFO] Running command: fastANI --query /var/lib/cwl/stga88ceb77-a78c-45ca-ad98-945b746ba859/GCF_016863115.1_ASM1686311v1_genomic.fna.gz --refList GCF_016863115.1_ASM1686311v1_genomic.fna/target_genomes.txt --output GCF_016863115.1_ASM1686311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:24,605] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:24,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:24,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:24,618] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:24,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:24,619] [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
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	100.0	1978	1984	95	conclusive
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	82.7683	1172	1984	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	82.6791	1200	1984	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	82.6356	1087	1984	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	82.6113	1181	1984	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	82.5494	1096	1984	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	82.4166	1112	1984	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	82.3888	1166	1984	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	82.27	1134	1984	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	82.2641	1119	1984	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	82.0969	1128	1984	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	81.8231	1020	1984	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	81.3983	1006	1984	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.5965	919	1984	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.4412	650	1984	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.0926	879	1984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:24,621] [INFO] DFAST Taxonomy check result was written to GCF_016863115.1_ASM1686311v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:24,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:24,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:24,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference/checkm_data
[2024-01-24 11:27:24,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:24,685] [INFO] Task started: CheckM
[2024-01-24 11:27:24,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863115.1_ASM1686311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863115.1_ASM1686311v1_genomic.fna/checkm_input GCF_016863115.1_ASM1686311v1_genomic.fna/checkm_result
[2024-01-24 11:28:17,618] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:17,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:17,642] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:17,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:17,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863115.1_ASM1686311v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:17,643] [INFO] Task started: Blastn
[2024-01-24 11:28:17,643] [INFO] Running command: blastn -query GCF_016863115.1_ASM1686311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc11bc187-587c-4e2b-add2-ca5ff42f727a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863115.1_ASM1686311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:19,526] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:19,530] [INFO] Selected 12 target genomes.
[2024-01-24 11:28:19,531] [INFO] Target genome list was writen to GCF_016863115.1_ASM1686311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:19,555] [INFO] Task started: fastANI
[2024-01-24 11:28:19,555] [INFO] Running command: fastANI --query /var/lib/cwl/stga88ceb77-a78c-45ca-ad98-945b746ba859/GCF_016863115.1_ASM1686311v1_genomic.fna.gz --refList GCF_016863115.1_ASM1686311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863115.1_ASM1686311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:39,348] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:39,370] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:39,371] [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_016863115.1	s__Sphaerimonospora thailandensis	100.0	1978	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerimonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001552515.1	s__Sphaerimonospora mesophila	89.0718	1328	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerimonospora	95.0	99.25	99.25	0.94	0.94	2	-
GCF_016863095.1	s__Microbispora siamensis	82.7886	1168	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006334915.2	s__Microbispora catharanthi	82.651	1175	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_014161445.1	s__Microbispora sp014161445	82.6203	1206	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_014647835.1	s__Microbispora aerata	82.5616	1094	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863035.1	s__Microbispora corallina	82.4417	1109	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
GCF_006874475.1	s__Microbispora hainanensis	82.3684	1171	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_016863015.1	s__Microbispora amethystogenes	82.2633	1135	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_012999535.1	s__Microbispora sp012999535	82.2482	1128	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003260025.2	s__Microbispora triticiradicis	82.2298	1089	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_016863335.1	s__Planotetraspora thailandica	81.3549	1013	1984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:39,372] [INFO] GTDB search result was written to GCF_016863115.1_ASM1686311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:39,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:39,377] [INFO] DFAST_QC result json was written to GCF_016863115.1_ASM1686311v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:39,377] [INFO] DFAST_QC completed!
[2024-01-24 11:28:39,377] [INFO] Total running time: 0h2m1s