[2024-01-24 11:34:43,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,004] [INFO] DQC Reference Directory: /var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference
[2024-01-24 11:34:44,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,438] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,439] [INFO] Running command: gunzip -c /var/lib/cwl/stg9db37517-7efb-4584-9491-d1c4a4099d0e/GCF_020215705.1_ASM2021570v1_genomic.fna.gz | prodigal -d GCF_020215705.1_ASM2021570v1_genomic.fna/cds.fna -a GCF_020215705.1_ASM2021570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:20,050] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:20,050] [INFO] Task started: HMMsearch
[2024-01-24 11:35:20,050] [INFO] Running command: hmmsearch --tblout GCF_020215705.1_ASM2021570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference/reference_markers.hmm GCF_020215705.1_ASM2021570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:20,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:20,532] [INFO] Found 6/6 markers.
[2024-01-24 11:35:20,621] [INFO] Query marker FASTA was written to GCF_020215705.1_ASM2021570v1_genomic.fna/markers.fasta
[2024-01-24 11:35:20,621] [INFO] Task started: Blastn
[2024-01-24 11:35:20,621] [INFO] Running command: blastn -query GCF_020215705.1_ASM2021570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference/reference_markers.fasta -out GCF_020215705.1_ASM2021570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:22,004] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:22,008] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:22,009] [INFO] Target genome list was writen to GCF_020215705.1_ASM2021570v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:22,020] [INFO] Task started: fastANI
[2024-01-24 11:35:22,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db37517-7efb-4584-9491-d1c4a4099d0e/GCF_020215705.1_ASM2021570v1_genomic.fna.gz --refList GCF_020215705.1_ASM2021570v1_genomic.fna/target_genomes.txt --output GCF_020215705.1_ASM2021570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:03,636] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:03,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:03,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:03,650] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:03,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:03,651] [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 aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	100.0	3875	3885	95	conclusive
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	90.6881	2933	3885	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	86.888	1357	3885	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	84.0458	1770	3885	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	84.0007	1758	3885	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	83.8771	1422	3885	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.6325	2227	3885	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	83.5573	2264	3885	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.4886	2114	3885	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	83.4503	1983	3885	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.3888	1811	3885	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.267	2121	3885	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	83.0178	1912	3885	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	83.004	2078	3885	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	82.7776	1969	3885	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	82.6549	1837	3885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:03,653] [INFO] DFAST Taxonomy check result was written to GCF_020215705.1_ASM2021570v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:03,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:03,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:03,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference/checkm_data
[2024-01-24 11:36:03,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:03,757] [INFO] Task started: CheckM
[2024-01-24 11:36:03,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020215705.1_ASM2021570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020215705.1_ASM2021570v1_genomic.fna/checkm_input GCF_020215705.1_ASM2021570v1_genomic.fna/checkm_result
[2024-01-24 11:37:40,761] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:40,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 6.13%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:40,792] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:40,793] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:40,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020215705.1_ASM2021570v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:40,794] [INFO] Task started: Blastn
[2024-01-24 11:37:40,794] [INFO] Running command: blastn -query GCF_020215705.1_ASM2021570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef5aaa85-5c80-4a84-83b5-f4f1c032aac4/dqc_reference/reference_markers_gtdb.fasta -out GCF_020215705.1_ASM2021570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:42,834] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:42,838] [INFO] Selected 17 target genomes.
[2024-01-24 11:37:42,839] [INFO] Target genome list was writen to GCF_020215705.1_ASM2021570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:42,851] [INFO] Task started: fastANI
[2024-01-24 11:37:42,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db37517-7efb-4584-9491-d1c4a4099d0e/GCF_020215705.1_ASM2021570v1_genomic.fna.gz --refList GCF_020215705.1_ASM2021570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020215705.1_ASM2021570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:28,455] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:28,481] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:38:28,482] [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_018603905.1	s__Nonomuraea sp018603905	90.7892	2896	3885	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	84.0151	1754	3885	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	83.6522	2224	3885	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	83.5591	2265	3885	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	83.5206	2099	3885	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	83.4638	2095	3885	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	83.4603	1982	3885	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	83.4207	1946	3885	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	83.3722	1814	3885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645445.1	s__Nonomuraea cypriaca	83.2875	1869	3885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	83.2208	2378	3885	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	83.0849	1918	3885	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	82.9736	2085	3885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_008086045.1	s__Nonomuraea sp008086045	82.776	2197	3885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	82.7441	1977	3885	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	82.6399	1839	3885	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	82.568	2090	3885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:28,483] [INFO] GTDB search result was written to GCF_020215705.1_ASM2021570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:28,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:28,490] [INFO] DFAST_QC result json was written to GCF_020215705.1_ASM2021570v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:28,491] [INFO] DFAST_QC completed!
[2024-01-24 11:38:28,491] [INFO] Total running time: 0h3m45s