[2024-01-24 13:55:46,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:46,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:46,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference
[2024-01-24 13:55:48,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:48,036] [INFO] Task started: Prodigal
[2024-01-24 13:55:48,037] [INFO] Running command: gunzip -c /var/lib/cwl/stga988b671-fc8b-4aea-a654-db64f0f73fb0/GCF_014873535.1_ASM1487353v1_genomic.fna.gz | prodigal -d GCF_014873535.1_ASM1487353v1_genomic.fna/cds.fna -a GCF_014873535.1_ASM1487353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:16,096] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:16,097] [INFO] Task started: HMMsearch
[2024-01-24 13:56:16,097] [INFO] Running command: hmmsearch --tblout GCF_014873535.1_ASM1487353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference/reference_markers.hmm GCF_014873535.1_ASM1487353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:16,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:16,500] [INFO] Found 6/6 markers.
[2024-01-24 13:56:16,585] [INFO] Query marker FASTA was written to GCF_014873535.1_ASM1487353v1_genomic.fna/markers.fasta
[2024-01-24 13:56:16,586] [INFO] Task started: Blastn
[2024-01-24 13:56:16,586] [INFO] Running command: blastn -query GCF_014873535.1_ASM1487353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference/reference_markers.fasta -out GCF_014873535.1_ASM1487353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:17,953] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:17,957] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:17,957] [INFO] Target genome list was writen to GCF_014873535.1_ASM1487353v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:17,977] [INFO] Task started: fastANI
[2024-01-24 13:56:17,978] [INFO] Running command: fastANI --query /var/lib/cwl/stga988b671-fc8b-4aea-a654-db64f0f73fb0/GCF_014873535.1_ASM1487353v1_genomic.fna.gz --refList GCF_014873535.1_ASM1487353v1_genomic.fna/target_genomes.txt --output GCF_014873535.1_ASM1487353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:08,137] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:08,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:08,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:08,158] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:08,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:08,159] [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 africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	100.0	3231	3231	95	conclusive
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	91.0009	2471	3231	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	82.2526	1759	3231	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	82.2374	1126	3231	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	82.1171	1503	3231	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	82.1166	1493	3231	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	81.9714	1752	3231	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	81.9141	1745	3231	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	81.9097	1747	3231	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	81.8644	1823	3231	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	81.8461	1755	3231	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	81.7959	1640	3231	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	81.6613	1728	3231	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	81.6128	1895	3231	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	81.603	1685	3231	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	81.5881	1681	3231	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	81.5549	1583	3231	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	81.5317	1589	3231	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	81.4581	1690	3231	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	81.2888	1726	3231	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	80.7765	1509	3231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:08,160] [INFO] DFAST Taxonomy check result was written to GCF_014873535.1_ASM1487353v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:08,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:08,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:08,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference/checkm_data
[2024-01-24 13:57:08,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:08,254] [INFO] Task started: CheckM
[2024-01-24 13:57:08,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873535.1_ASM1487353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873535.1_ASM1487353v1_genomic.fna/checkm_input GCF_014873535.1_ASM1487353v1_genomic.fna/checkm_result
[2024-01-24 13:58:46,824] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:46,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.60%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,852] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:46,853] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:46,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873535.1_ASM1487353v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:46,854] [INFO] Task started: Blastn
[2024-01-24 13:58:46,854] [INFO] Running command: blastn -query GCF_014873535.1_ASM1487353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4049d3d3-7d5c-4870-a8cc-8fa8136f2d0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873535.1_ASM1487353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,083] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:49,083] [INFO] Target genome list was writen to GCF_014873535.1_ASM1487353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,101] [INFO] Task started: fastANI
[2024-01-24 13:58:49,102] [INFO] Running command: fastANI --query /var/lib/cwl/stga988b671-fc8b-4aea-a654-db64f0f73fb0/GCF_014873535.1_ASM1487353v1_genomic.fna.gz --refList GCF_014873535.1_ASM1487353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873535.1_ASM1487353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:45,738] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:45,756] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:45,756] [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_014873535.1	s__Nonomuraea africana	100.0	3231	3231	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_014195505.1	s__Nonomuraea dietziae	90.9689	2477	3231	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	82.5647	805	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	82.277	1757	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	82.1467	1488	3231	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	82.1001	1637	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093975.1	s__Nonomuraea rubra_A	81.8978	1596	3231	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	81.8976	1763	3231	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	81.8758	1755	3231	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	81.8246	1761	3231	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	81.8162	1830	3231	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	81.8094	1637	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_000725485.1	s__Nonomuraea candida	81.743	1762	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760925.1	s__Nonomuraea typhae	81.6309	1841	3231	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	81.6287	1891	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	81.6205	1784	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_900111685.1	s__Nonomuraea wenchangensis	81.4845	1684	3231	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	81.4726	1639	3231	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	81.4713	1860	3231	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	81.4616	1830	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	81.2763	1731	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	80.7339	1518	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_014202315.1	s__Thermocatellispora tengchongensis	80.2504	1592	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:45,758] [INFO] GTDB search result was written to GCF_014873535.1_ASM1487353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:45,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:45,763] [INFO] DFAST_QC result json was written to GCF_014873535.1_ASM1487353v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:45,764] [INFO] DFAST_QC completed!
[2024-01-24 13:59:45,764] [INFO] Total running time: 0h3m59s