[2024-01-25 19:24:45,035] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference
[2024-01-25 19:24:48,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,897] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg900514fe-eaa9-4b9d-b795-e124b9392805/GCF_003990035.1_ASM399003v1_genomic.fna.gz | prodigal -d GCF_003990035.1_ASM399003v1_genomic.fna/cds.fna -a GCF_003990035.1_ASM399003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:58,682] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:58,683] [INFO] Task started: HMMsearch
[2024-01-25 19:24:58,683] [INFO] Running command: hmmsearch --tblout GCF_003990035.1_ASM399003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference/reference_markers.hmm GCF_003990035.1_ASM399003v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:58,936] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:58,937] [INFO] Found 6/6 markers.
[2024-01-25 19:24:58,969] [INFO] Query marker FASTA was written to GCF_003990035.1_ASM399003v1_genomic.fna/markers.fasta
[2024-01-25 19:24:58,970] [INFO] Task started: Blastn
[2024-01-25 19:24:58,970] [INFO] Running command: blastn -query GCF_003990035.1_ASM399003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference/reference_markers.fasta -out GCF_003990035.1_ASM399003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:00,070] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:00,074] [INFO] Selected 11 target genomes.
[2024-01-25 19:25:00,074] [INFO] Target genome list was writen to GCF_003990035.1_ASM399003v1_genomic.fna/target_genomes.txt
[2024-01-25 19:25:00,147] [INFO] Task started: fastANI
[2024-01-25 19:25:00,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg900514fe-eaa9-4b9d-b795-e124b9392805/GCF_003990035.1_ASM399003v1_genomic.fna.gz --refList GCF_003990035.1_ASM399003v1_genomic.fna/target_genomes.txt --output GCF_003990035.1_ASM399003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:08,478] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:08,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:08,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:08,486] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:08,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:08,487] [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
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	100.0	1275	1276	95	conclusive
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	99.9981	1276	1276	95	conclusive
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	84.5604	927	1276	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	82.9494	812	1276	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	82.6424	768	1276	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.8768	414	1276	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.79	429	1276	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.7497	456	1276	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.7141	422	1276	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.6786	415	1276	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.5469	421	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:08,488] [INFO] DFAST Taxonomy check result was written to GCF_003990035.1_ASM399003v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:08,489] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:08,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:08,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference/checkm_data
[2024-01-25 19:25:08,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:08,530] [INFO] Task started: CheckM
[2024-01-25 19:25:08,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990035.1_ASM399003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990035.1_ASM399003v1_genomic.fna/checkm_input GCF_003990035.1_ASM399003v1_genomic.fna/checkm_result
[2024-01-25 19:26:02,394] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:02,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:02,412] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:02,412] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:02,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990035.1_ASM399003v1_genomic.fna/markers.fasta)
[2024-01-25 19:26:02,414] [INFO] Task started: Blastn
[2024-01-25 19:26:02,414] [INFO] Running command: blastn -query GCF_003990035.1_ASM399003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9123ae3a-9cf6-4a7b-8e1c-5cb715f1b2ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990035.1_ASM399003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:04,223] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:04,226] [INFO] Selected 12 target genomes.
[2024-01-25 19:26:04,226] [INFO] Target genome list was writen to GCF_003990035.1_ASM399003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:04,273] [INFO] Task started: fastANI
[2024-01-25 19:26:04,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg900514fe-eaa9-4b9d-b795-e124b9392805/GCF_003990035.1_ASM399003v1_genomic.fna.gz --refList GCF_003990035.1_ASM399003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990035.1_ASM399003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:26:13,543] [INFO] Task succeeded: fastANI
[2024-01-25 19:26:13,552] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:26:13,552] [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_003014675.1	s__Labedella gwakjiensis	99.9981	1276	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003990045.1	s__Labedella endophytica	84.5902	925	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078635.1	s__Labedella phragmitis	82.9496	812	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078655.1	s__Labedella populi	82.6744	765	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984125.1	s__Okibacterium sp001984125	78.8247	410	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710805.1	s__Agromyces tardus	78.8042	478	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	78.6603	430	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240565.1	s__Clavibacter insidiosus	78.6041	420	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	-
GCF_009789225.1	s__WSTA01 sp009789225	78.5386	446	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570845.1	s__Leifsonia_A flava	78.4209	417	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	-
GCF_004801905.1	s__Leifsonia_A flavus	78.3592	350	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	78.1251	386	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:26:13,555] [INFO] GTDB search result was written to GCF_003990035.1_ASM399003v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:26:13,556] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:26:13,560] [INFO] DFAST_QC result json was written to GCF_003990035.1_ASM399003v1_genomic.fna/dqc_result.json
[2024-01-25 19:26:13,560] [INFO] DFAST_QC completed!
[2024-01-25 19:26:13,560] [INFO] Total running time: 0h1m29s