[2024-01-24 13:40:55,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference
[2024-01-24 13:40:56,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,493] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,493] [INFO] Running command: gunzip -c /var/lib/cwl/stg0633541c-26a9-4a6c-9f6f-a9dc75b92a16/GCF_014195505.1_ASM1419550v1_genomic.fna.gz | prodigal -d GCF_014195505.1_ASM1419550v1_genomic.fna/cds.fna -a GCF_014195505.1_ASM1419550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:27,179] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:27,180] [INFO] Task started: HMMsearch
[2024-01-24 13:41:27,180] [INFO] Running command: hmmsearch --tblout GCF_014195505.1_ASM1419550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference/reference_markers.hmm GCF_014195505.1_ASM1419550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:27,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:27,621] [INFO] Found 6/6 markers.
[2024-01-24 13:41:27,698] [INFO] Query marker FASTA was written to GCF_014195505.1_ASM1419550v1_genomic.fna/markers.fasta
[2024-01-24 13:41:27,699] [INFO] Task started: Blastn
[2024-01-24 13:41:27,699] [INFO] Running command: blastn -query GCF_014195505.1_ASM1419550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference/reference_markers.fasta -out GCF_014195505.1_ASM1419550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,174] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,178] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:29,179] [INFO] Target genome list was writen to GCF_014195505.1_ASM1419550v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,188] [INFO] Task started: fastANI
[2024-01-24 13:41:29,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg0633541c-26a9-4a6c-9f6f-a9dc75b92a16/GCF_014195505.1_ASM1419550v1_genomic.fna.gz --refList GCF_014195505.1_ASM1419550v1_genomic.fna/target_genomes.txt --output GCF_014195505.1_ASM1419550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:22,982] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:22,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:22,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:22,999] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:23,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:23,000] [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 dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	100.0	3413	3413	95	conclusive
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	90.9778	2467	3413	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	82.0056	1148	3413	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	81.9816	1837	3413	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	81.8257	1549	3413	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	81.8096	1846	3413	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	81.8017	1803	3413	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	81.7935	1567	3413	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	81.6939	1804	3413	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	81.6729	1876	3413	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	81.6558	1840	3413	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	81.6436	1868	3413	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	81.6425	1696	3413	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	81.5979	1956	3413	95	below_threshold
Nonomuraea glycinis	strain=CGMCC 4.7430	GCA_014646515.1	2047744	2047744	type	True	81.5853	1699	3413	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	81.5794	1908	3413	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	81.5517	1723	3413	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	81.5381	1873	3413	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	81.3949	1599	3413	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	81.364	1578	3413	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	80.6985	1577	3413	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	80.6512	1529	3413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:23,002] [INFO] DFAST Taxonomy check result was written to GCF_014195505.1_ASM1419550v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:23,002] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:23,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:23,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference/checkm_data
[2024-01-24 13:42:23,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:23,090] [INFO] Task started: CheckM
[2024-01-24 13:42:23,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195505.1_ASM1419550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195505.1_ASM1419550v1_genomic.fna/checkm_input GCF_014195505.1_ASM1419550v1_genomic.fna/checkm_result
[2024-01-24 13:43:58,179] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:58,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:58,207] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:58,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:58,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195505.1_ASM1419550v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:58,208] [INFO] Task started: Blastn
[2024-01-24 13:43:58,208] [INFO] Running command: blastn -query GCF_014195505.1_ASM1419550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48711e7b-6137-4888-a4a7-26b5f881016d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195505.1_ASM1419550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:00,314] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:00,321] [INFO] Selected 21 target genomes.
[2024-01-24 13:44:00,321] [INFO] Target genome list was writen to GCF_014195505.1_ASM1419550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:00,346] [INFO] Task started: fastANI
[2024-01-24 13:44:00,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg0633541c-26a9-4a6c-9f6f-a9dc75b92a16/GCF_014195505.1_ASM1419550v1_genomic.fna.gz --refList GCF_014195505.1_ASM1419550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195505.1_ASM1419550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:50,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:50,870] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:50,871] [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_014195505.1	s__Nonomuraea dietziae	100.0	3413	3413	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_014873535.1	s__Nonomuraea africana	90.9704	2468	3413	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	82.6921	823	3413	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	81.9623	1690	3413	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	81.9591	1823	3413	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	81.8454	1556	3413	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	81.8086	1920	3413	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	81.7756	1856	3413	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	81.6925	1804	3413	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	81.6764	1886	3413	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	81.6035	1951	3413	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	81.6032	1662	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646515.1	s__Nonomuraea glycinis	81.597	1697	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	81.5778	1717	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334985.2	s__Nonomuraea phyllanthi	81.5299	1765	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_004348995.1	s__Nonomuraea terrae	81.4151	1596	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	81.393	1568	3413	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	81.3622	1951	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_008086045.1	s__Nonomuraea sp008086045	81.2962	1932	3413	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	80.6713	1585	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	80.6427	1529	3413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:50,872] [INFO] GTDB search result was written to GCF_014195505.1_ASM1419550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:50,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:50,876] [INFO] DFAST_QC result json was written to GCF_014195505.1_ASM1419550v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:50,877] [INFO] DFAST_QC completed!
[2024-01-24 13:44:50,877] [INFO] Total running time: 0h3m56s