[2024-01-24 10:47:40,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,967] [INFO] DQC Reference Directory: /var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference
[2024-01-24 10:47:44,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,787] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg635e192a-84a9-49a4-83c1-4ba7aaabfb9a/GCF_020215905.1_ASM2021590v1_genomic.fna.gz | prodigal -d GCF_020215905.1_ASM2021590v1_genomic.fna/cds.fna -a GCF_020215905.1_ASM2021590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:07,263] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:07,264] [INFO] Task started: HMMsearch
[2024-01-24 10:48:07,264] [INFO] Running command: hmmsearch --tblout GCF_020215905.1_ASM2021590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference/reference_markers.hmm GCF_020215905.1_ASM2021590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:07,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:07,632] [INFO] Found 6/6 markers.
[2024-01-24 10:48:07,697] [INFO] Query marker FASTA was written to GCF_020215905.1_ASM2021590v1_genomic.fna/markers.fasta
[2024-01-24 10:48:07,698] [INFO] Task started: Blastn
[2024-01-24 10:48:07,698] [INFO] Running command: blastn -query GCF_020215905.1_ASM2021590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference/reference_markers.fasta -out GCF_020215905.1_ASM2021590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:09,071] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:09,076] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:09,076] [INFO] Target genome list was writen to GCF_020215905.1_ASM2021590v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:09,096] [INFO] Task started: fastANI
[2024-01-24 10:48:09,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg635e192a-84a9-49a4-83c1-4ba7aaabfb9a/GCF_020215905.1_ASM2021590v1_genomic.fna.gz --refList GCF_020215905.1_ASM2021590v1_genomic.fna/target_genomes.txt --output GCF_020215905.1_ASM2021590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:52,359] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:52,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:52,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:52,376] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:52,377] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:52,377] [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
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	100.0	2673	2677	95	conclusive
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	99.979	2650	2677	95	conclusive
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	84.9968	1318	2677	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	84.8587	1718	2677	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	84.7025	1641	2677	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	84.2787	1716	2677	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	84.2402	1682	2677	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	84.2324	1666	2677	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.2321	1153	2677	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	84.1523	1759	2677	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	84.0054	1751	2677	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	83.6233	1770	2677	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.5796	1739	2677	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.5252	1681	2677	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	83.4913	1590	2677	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.4239	1726	2677	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	83.1635	1699	2677	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	83.0896	1582	2677	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	79.7475	1135	2677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:52,379] [INFO] DFAST Taxonomy check result was written to GCF_020215905.1_ASM2021590v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:52,379] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:52,379] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:52,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference/checkm_data
[2024-01-24 10:48:52,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:52,454] [INFO] Task started: CheckM
[2024-01-24 10:48:52,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020215905.1_ASM2021590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020215905.1_ASM2021590v1_genomic.fna/checkm_input GCF_020215905.1_ASM2021590v1_genomic.fna/checkm_result
[2024-01-24 10:50:03,302] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:03,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.06%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:03,334] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:03,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:03,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020215905.1_ASM2021590v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:03,335] [INFO] Task started: Blastn
[2024-01-24 10:50:03,336] [INFO] Running command: blastn -query GCF_020215905.1_ASM2021590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3f4776e-4d75-48f4-9e6a-beb89663cf50/dqc_reference/reference_markers_gtdb.fasta -out GCF_020215905.1_ASM2021590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:05,482] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:05,486] [INFO] Selected 22 target genomes.
[2024-01-24 10:50:05,487] [INFO] Target genome list was writen to GCF_020215905.1_ASM2021590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:05,517] [INFO] Task started: fastANI
[2024-01-24 10:50:05,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg635e192a-84a9-49a4-83c1-4ba7aaabfb9a/GCF_020215905.1_ASM2021590v1_genomic.fna.gz --refList GCF_020215905.1_ASM2021590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020215905.1_ASM2021590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:58,169] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:58,191] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:58,191] [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_014646355.1	s__Nonomuraea cavernae	99.9807	2649	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014207745.1	s__Nonomuraea muscovyensis	84.8752	1715	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	84.6813	1645	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362835.1	s__Nonomuraea sp013362835	84.5175	790	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	84.2532	1610	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	84.2223	1667	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	84.195	1690	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603905.1	s__Nonomuraea sp018603905	84.1624	1753	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017515.1	s__Nonomuraea sp008017515	83.986	1775	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889725.1	s__Nonomuraea zeae	83.6348	1767	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	83.5789	1672	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	83.5527	1748	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	83.4336	1619	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	83.4212	1744	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	83.3246	1781	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	83.321	1742	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	83.2953	1693	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	83.1775	1778	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	83.1638	1700	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	83.0468	1590	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_018531495.1	s__Nonomuraea sp018531495	82.7775	1609	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001570385.1	s__Microtetraspora glauca	79.9005	1235	2677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:58,193] [INFO] GTDB search result was written to GCF_020215905.1_ASM2021590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:58,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:58,197] [INFO] DFAST_QC result json was written to GCF_020215905.1_ASM2021590v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:58,198] [INFO] DFAST_QC completed!
[2024-01-24 10:50:58,198] [INFO] Total running time: 0h3m17s