[2024-01-24 13:32:56,679] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference
[2024-01-24 13:32:57,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,897] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd5f8a8a-919a-4c89-8541-df09063aeb54/GCF_019049105.1_ASM1904910v1_genomic.fna.gz | prodigal -d GCF_019049105.1_ASM1904910v1_genomic.fna/cds.fna -a GCF_019049105.1_ASM1904910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:06,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:06,939] [INFO] Task started: HMMsearch
[2024-01-24 13:33:06,939] [INFO] Running command: hmmsearch --tblout GCF_019049105.1_ASM1904910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference/reference_markers.hmm GCF_019049105.1_ASM1904910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:07,194] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:07,195] [INFO] Found 6/6 markers.
[2024-01-24 13:33:07,222] [INFO] Query marker FASTA was written to GCF_019049105.1_ASM1904910v1_genomic.fna/markers.fasta
[2024-01-24 13:33:07,222] [INFO] Task started: Blastn
[2024-01-24 13:33:07,222] [INFO] Running command: blastn -query GCF_019049105.1_ASM1904910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference/reference_markers.fasta -out GCF_019049105.1_ASM1904910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:07,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:07,929] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:07,929] [INFO] Target genome list was writen to GCF_019049105.1_ASM1904910v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:08,093] [INFO] Task started: fastANI
[2024-01-24 13:33:08,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5f8a8a-919a-4c89-8541-df09063aeb54/GCF_019049105.1_ASM1904910v1_genomic.fna.gz --refList GCF_019049105.1_ASM1904910v1_genomic.fna/target_genomes.txt --output GCF_019049105.1_ASM1904910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:21,809] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:21,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:21,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:21,832] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:21,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:21,832] [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
Leucobacter chinensis	strain=NC76-1	GCA_019049105.1	2851010	2851010	type	True	100.0	968	968	95	conclusive
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	78.0376	207	968	95	below_threshold
Leucobacter exalbidus	strain=DSM 22850	GCA_017834145.1	662960	662960	type	True	77.9181	178	968	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	77.8889	188	968	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	77.8852	211	968	95	below_threshold
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	77.7785	238	968	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	77.7165	203	968	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	77.7103	209	968	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	77.2405	133	968	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	77.1025	121	968	95	below_threshold
Pseudoclavibacter alba	strain=NBRC 15616	GCA_001570905.1	272241	272241	type	True	77.1023	76	968	95	below_threshold
Lysinibacter cavernae	strain=DSM 27960	GCA_011758565.1	1640652	1640652	type	True	77.0876	91	968	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	76.9366	126	968	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	76.9331	123	968	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	76.8785	159	968	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	76.8771	146	968	95	below_threshold
Mycetocola zhadangensis	strain=ZD1-4	GCA_003668565.1	1164595	1164595	type	True	76.8327	70	968	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	76.8294	127	968	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_004134805.1	592376	592376	type	True	76.8193	126	968	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	76.7893	124	968	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	76.769	104	968	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	76.7228	117	968	95	below_threshold
Glaciibacter superstes	strain=DSM 21135	GCA_000421145.1	501023	501023	type	True	76.6219	68	968	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	76.164	89	968	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.0513	78	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,834] [INFO] DFAST Taxonomy check result was written to GCF_019049105.1_ASM1904910v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:21,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:21,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:21,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference/checkm_data
[2024-01-24 13:33:21,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:21,866] [INFO] Task started: CheckM
[2024-01-24 13:33:21,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019049105.1_ASM1904910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019049105.1_ASM1904910v1_genomic.fna/checkm_input GCF_019049105.1_ASM1904910v1_genomic.fna/checkm_result
[2024-01-24 13:33:52,586] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:52,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:52,609] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:52,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:52,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019049105.1_ASM1904910v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:52,610] [INFO] Task started: Blastn
[2024-01-24 13:33:52,610] [INFO] Running command: blastn -query GCF_019049105.1_ASM1904910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056da611-32ca-4b0f-ba78-3013c115868a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019049105.1_ASM1904910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:53,634] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:53,639] [INFO] Selected 24 target genomes.
[2024-01-24 13:33:53,639] [INFO] Target genome list was writen to GCF_019049105.1_ASM1904910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:53,691] [INFO] Task started: fastANI
[2024-01-24 13:33:53,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5f8a8a-919a-4c89-8541-df09063aeb54/GCF_019049105.1_ASM1904910v1_genomic.fna.gz --refList GCF_019049105.1_ASM1904910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019049105.1_ASM1904910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:07,323] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:07,353] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:07,354] [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_019049105.1	s__NC76-1 sp019049105	100.0	968	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__NC76-1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014530035.1	s__Leucobacter sp014530035	78.1235	143	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004028235.1	s__Leucobacter muris	78.0549	206	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_017834145.1	s__Leucobacter exalbidus	77.9181	178	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421845.1	s__Leucobacter chironomi	77.8905	212	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350525.1	s__Leucobacter salsicius	77.8889	188	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	77.8273	192	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716085.1	s__Leucobacter komagatae	77.7785	238	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522535.1	s__Leucobacter sp016522535	77.7662	191	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161405.1	s__Cx-87 sp014529995	77.7496	181	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cx-87	95.0	98.78	98.17	0.90	0.87	4	-
GCF_016758255.1	s__Leucobacter chromiireducens	77.7329	198	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102345.1	s__Leucobacter chromiiresistens	77.7103	209	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_000633415.1	s__Leucobacter sp000633415	77.7065	228	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980875.1	s__Leucobacter sp000980875	77.5485	217	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569785.1	s__Leucobacter sp003569785	77.4009	182	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597785.1	s__Leucobacter sp001373475	77.2916	177	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.62	98.46	0.91	0.89	3	-
GCF_001542775.1	s__Microterricola viridarii_A	77.1241	118	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716125.1	s__Homoserinimonas aerilata	76.9548	78	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070885.1	s__Agromyces badenianii	76.9165	127	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_001314225.1	s__Microbacterium sp001314225	76.8561	151	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907835.1	s__Agromyces cerinus_A	76.7876	147	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807485.1	s__Microbacterium sp016807485	76.6986	71	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421145.1	s__Glaciibacter superstes	76.5891	69	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000878135.1	s__Frigoribacterium sp000878135	76.5401	93	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	98.53	98.34	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:07,355] [INFO] GTDB search result was written to GCF_019049105.1_ASM1904910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:07,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:07,364] [INFO] DFAST_QC result json was written to GCF_019049105.1_ASM1904910v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:07,365] [INFO] DFAST_QC completed!
[2024-01-24 13:34:07,365] [INFO] Total running time: 0h1m11s