[2024-01-24 14:55:50,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference
[2024-01-24 14:55:52,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,394] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ceeebd7-e9a3-4154-97ed-c7d6d0f8501d/GCF_014203235.1_ASM1420323v1_genomic.fna.gz | prodigal -d GCF_014203235.1_ASM1420323v1_genomic.fna/cds.fna -a GCF_014203235.1_ASM1420323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:24,598] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:24,599] [INFO] Task started: HMMsearch
[2024-01-24 14:56:24,599] [INFO] Running command: hmmsearch --tblout GCF_014203235.1_ASM1420323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference/reference_markers.hmm GCF_014203235.1_ASM1420323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:25,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:25,057] [INFO] Found 6/6 markers.
[2024-01-24 14:56:25,146] [INFO] Query marker FASTA was written to GCF_014203235.1_ASM1420323v1_genomic.fna/markers.fasta
[2024-01-24 14:56:25,146] [INFO] Task started: Blastn
[2024-01-24 14:56:25,147] [INFO] Running command: blastn -query GCF_014203235.1_ASM1420323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference/reference_markers.fasta -out GCF_014203235.1_ASM1420323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:26,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:26,514] [INFO] Selected 21 target genomes.
[2024-01-24 14:56:26,514] [INFO] Target genome list was writen to GCF_014203235.1_ASM1420323v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:26,522] [INFO] Task started: fastANI
[2024-01-24 14:56:26,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ceeebd7-e9a3-4154-97ed-c7d6d0f8501d/GCF_014203235.1_ASM1420323v1_genomic.fna.gz --refList GCF_014203235.1_ASM1420323v1_genomic.fna/target_genomes.txt --output GCF_014203235.1_ASM1420323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:21,471] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:21,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:21,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:21,491] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:57:21,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:21,492] [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 endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	100.0	3795	3800	95	conclusive
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	86.7879	2689	3800	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	82.4397	1221	3800	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	82.0921	1978	3800	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	82.062	1617	3800	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	82.0254	1619	3800	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	81.9383	1891	3800	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	81.9017	1803	3800	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	81.7943	1780	3800	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	81.7893	1872	3800	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	81.786	1770	3800	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	81.7832	1926	3800	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	81.7433	1874	3800	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	81.6736	1738	3800	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	81.6611	1921	3800	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	81.6202	1709	3800	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	81.5702	1819	3800	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	81.5118	1882	3800	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	81.4572	2018	3800	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	81.3078	1578	3800	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	78.6963	1108	3800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:21,493] [INFO] DFAST Taxonomy check result was written to GCF_014203235.1_ASM1420323v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:21,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:21,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:21,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference/checkm_data
[2024-01-24 14:57:21,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:21,599] [INFO] Task started: CheckM
[2024-01-24 14:57:21,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203235.1_ASM1420323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203235.1_ASM1420323v1_genomic.fna/checkm_input GCF_014203235.1_ASM1420323v1_genomic.fna/checkm_result
[2024-01-24 14:59:10,160] [INFO] Task succeeded: CheckM
[2024-01-24 14:59:10,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 22.80%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 14:59:10,198] [INFO] ===== Completeness check finished =====
[2024-01-24 14:59:10,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:59:10,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203235.1_ASM1420323v1_genomic.fna/markers.fasta)
[2024-01-24 14:59:10,199] [INFO] Task started: Blastn
[2024-01-24 14:59:10,199] [INFO] Running command: blastn -query GCF_014203235.1_ASM1420323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c094e37-b785-40af-a16b-3e166f706943/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203235.1_ASM1420323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:59:12,450] [INFO] Task succeeded: Blastn
[2024-01-24 14:59:12,455] [INFO] Selected 19 target genomes.
[2024-01-24 14:59:12,455] [INFO] Target genome list was writen to GCF_014203235.1_ASM1420323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:59:12,481] [INFO] Task started: fastANI
[2024-01-24 14:59:12,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ceeebd7-e9a3-4154-97ed-c7d6d0f8501d/GCF_014203235.1_ASM1420323v1_genomic.fna.gz --refList GCF_014203235.1_ASM1420323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203235.1_ASM1420323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:00:00,461] [INFO] Task succeeded: fastANI
[2024-01-24 15:00:00,480] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:00:00,480] [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_014203235.1	s__Nonomuraea endophytica	100.0	3795	3800	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_009760925.1	s__Nonomuraea typhae	86.7709	2693	3800	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	82.8301	869	3800	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	82.129	1604	3800	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	82.1168	1827	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	82.1103	2111	3800	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	82.0527	1987	3800	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	81.9068	1804	3800	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	81.8191	1718	3800	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	81.8142	2013	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_000379885.1	s__Nonomuraea coxensis	81.7793	1771	3800	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	81.7511	1872	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	81.6342	1930	3800	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	81.5351	1827	3800	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	81.5188	1752	3800	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	81.5137	1953	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100395.1	s__Nonomuraea maritima	81.2818	1584	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013761175.1	s__Nonomuraea soli	81.0854	1910	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017896165.1	s__Microbispora sp017896165	78.6839	1113	3800	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:00:00,482] [INFO] GTDB search result was written to GCF_014203235.1_ASM1420323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:00:00,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:00:00,487] [INFO] DFAST_QC result json was written to GCF_014203235.1_ASM1420323v1_genomic.fna/dqc_result.json
[2024-01-24 15:00:00,487] [INFO] DFAST_QC completed!
[2024-01-24 15:00:00,487] [INFO] Total running time: 0h4m10s