[2024-01-25 20:21:20,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:20,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:20,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference
[2024-01-25 20:21:21,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:21,726] [INFO] Task started: Prodigal
[2024-01-25 20:21:21,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf3ca1f5-18c3-498b-a9d7-25bc887cf910/GCF_003014675.1_ASM301467v1_genomic.fna.gz | prodigal -d GCF_003014675.1_ASM301467v1_genomic.fna/cds.fna -a GCF_003014675.1_ASM301467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:31,336] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:31,336] [INFO] Task started: HMMsearch
[2024-01-25 20:21:31,336] [INFO] Running command: hmmsearch --tblout GCF_003014675.1_ASM301467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference/reference_markers.hmm GCF_003014675.1_ASM301467v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:31,555] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:31,556] [INFO] Found 6/6 markers.
[2024-01-25 20:21:31,587] [INFO] Query marker FASTA was written to GCF_003014675.1_ASM301467v1_genomic.fna/markers.fasta
[2024-01-25 20:21:31,588] [INFO] Task started: Blastn
[2024-01-25 20:21:31,588] [INFO] Running command: blastn -query GCF_003014675.1_ASM301467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference/reference_markers.fasta -out GCF_003014675.1_ASM301467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:32,671] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:32,674] [INFO] Selected 11 target genomes.
[2024-01-25 20:21:32,674] [INFO] Target genome list was writen to GCF_003014675.1_ASM301467v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:32,693] [INFO] Task started: fastANI
[2024-01-25 20:21:32,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf3ca1f5-18c3-498b-a9d7-25bc887cf910/GCF_003014675.1_ASM301467v1_genomic.fna.gz --refList GCF_003014675.1_ASM301467v1_genomic.fna/target_genomes.txt --output GCF_003014675.1_ASM301467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:41,252] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:41,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:41,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:41,260] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:21:41,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:41,261] [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=DSM 21548	GCA_003014675.1	390269	390269	type	True	100.0	1279	1279	95	conclusive
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	99.9941	1273	1279	95	conclusive
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	84.5045	937	1279	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	83.0722	797	1279	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	82.7312	753	1279	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.8902	398	1279	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.8171	416	1279	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.7435	426	1279	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.6721	430	1279	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.6131	400	1279	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.6028	464	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:41,262] [INFO] DFAST Taxonomy check result was written to GCF_003014675.1_ASM301467v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:41,262] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:41,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:41,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference/checkm_data
[2024-01-25 20:21:41,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:41,301] [INFO] Task started: CheckM
[2024-01-25 20:21:41,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014675.1_ASM301467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014675.1_ASM301467v1_genomic.fna/checkm_input GCF_003014675.1_ASM301467v1_genomic.fna/checkm_result
[2024-01-25 20:22:39,484] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:39,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:39,500] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:39,501] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:39,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014675.1_ASM301467v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:39,502] [INFO] Task started: Blastn
[2024-01-25 20:22:39,502] [INFO] Running command: blastn -query GCF_003014675.1_ASM301467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99bccb64-bddb-4c74-861c-c8529db6e55b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014675.1_ASM301467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:41,322] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:41,325] [INFO] Selected 12 target genomes.
[2024-01-25 20:22:41,325] [INFO] Target genome list was writen to GCF_003014675.1_ASM301467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:41,334] [INFO] Task started: fastANI
[2024-01-25 20:22:41,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf3ca1f5-18c3-498b-a9d7-25bc887cf910/GCF_003014675.1_ASM301467v1_genomic.fna.gz --refList GCF_003014675.1_ASM301467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014675.1_ASM301467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:50,774] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:50,782] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:50,783] [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	100.0	1279	1279	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	84.5151	936	1279	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	83.0487	800	1279	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	82.7396	752	1279	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	79.0072	398	1279	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	78.9717	463	1279	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	78.7081	421	1279	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	78.6895	405	1279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	-
GCF_004570845.1	s__Leifsonia_A flava	78.6647	393	1279	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	78.6266	342	1279	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_009789225.1	s__WSTA01 sp009789225	78.5235	438	1279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	78.0149	391	1279	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 20:22:50,784] [INFO] GTDB search result was written to GCF_003014675.1_ASM301467v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:50,784] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:50,787] [INFO] DFAST_QC result json was written to GCF_003014675.1_ASM301467v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:50,787] [INFO] DFAST_QC completed!
[2024-01-25 20:22:50,787] [INFO] Total running time: 0h1m30s