[2024-01-24 12:29:21,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:21,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:21,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference
[2024-01-24 12:29:22,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:22,981] [INFO] Task started: Prodigal
[2024-01-24 12:29:22,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg2aa1040a-9d9a-4e6a-8669-2ac1777ebcd0/GCF_004078635.1_ASM407863v1_genomic.fna.gz | prodigal -d GCF_004078635.1_ASM407863v1_genomic.fna/cds.fna -a GCF_004078635.1_ASM407863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:32,542] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:32,542] [INFO] Task started: HMMsearch
[2024-01-24 12:29:32,543] [INFO] Running command: hmmsearch --tblout GCF_004078635.1_ASM407863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference/reference_markers.hmm GCF_004078635.1_ASM407863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:32,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:32,785] [INFO] Found 6/6 markers.
[2024-01-24 12:29:32,821] [INFO] Query marker FASTA was written to GCF_004078635.1_ASM407863v1_genomic.fna/markers.fasta
[2024-01-24 12:29:32,822] [INFO] Task started: Blastn
[2024-01-24 12:29:32,822] [INFO] Running command: blastn -query GCF_004078635.1_ASM407863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference/reference_markers.fasta -out GCF_004078635.1_ASM407863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:34,044] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:34,047] [INFO] Selected 12 target genomes.
[2024-01-24 12:29:34,048] [INFO] Target genome list was writen to GCF_004078635.1_ASM407863v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:34,053] [INFO] Task started: fastANI
[2024-01-24 12:29:34,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa1040a-9d9a-4e6a-8669-2ac1777ebcd0/GCF_004078635.1_ASM407863v1_genomic.fna.gz --refList GCF_004078635.1_ASM407863v1_genomic.fna/target_genomes.txt --output GCF_004078635.1_ASM407863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:43,084] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:43,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:43,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:43,096] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:43,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:43,097] [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 phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	100.0	1167	1167	95	conclusive
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	86.7956	922	1167	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	83.0061	805	1167	95	below_threshold
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	82.9479	794	1167	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	82.7486	803	1167	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.0673	391	1167	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0298	431	1167	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.0177	396	1167	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.7066	392	1167	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.597	436	1167	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.4633	401	1167	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	78.0202	371	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:43,098] [INFO] DFAST Taxonomy check result was written to GCF_004078635.1_ASM407863v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:43,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:43,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:43,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference/checkm_data
[2024-01-24 12:29:43,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:43,142] [INFO] Task started: CheckM
[2024-01-24 12:29:43,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004078635.1_ASM407863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004078635.1_ASM407863v1_genomic.fna/checkm_input GCF_004078635.1_ASM407863v1_genomic.fna/checkm_result
[2024-01-24 12:30:29,341] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:29,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:29,365] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:29,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:29,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004078635.1_ASM407863v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:29,366] [INFO] Task started: Blastn
[2024-01-24 12:30:29,366] [INFO] Running command: blastn -query GCF_004078635.1_ASM407863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1da155b4-0de1-4112-85c7-d91652668f9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004078635.1_ASM407863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:31,508] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:31,512] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:31,513] [INFO] Target genome list was writen to GCF_004078635.1_ASM407863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:31,529] [INFO] Task started: fastANI
[2024-01-24 12:30:31,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa1040a-9d9a-4e6a-8669-2ac1777ebcd0/GCF_004078635.1_ASM407863v1_genomic.fna.gz --refList GCF_004078635.1_ASM407863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004078635.1_ASM407863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:41,076] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:41,093] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:41,093] [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_004078635.1	s__Labedella phragmitis	100.0	1167	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004078655.1	s__Labedella populi	86.8088	921	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014675.1	s__Labedella gwakjiensis	82.9639	793	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003990045.1	s__Labedella endophytica	82.7283	805	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	79.0043	434	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	78.7226	437	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789225.1	s__WSTA01 sp009789225	78.6913	444	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801905.1	s__Leifsonia_A flavus	78.6781	323	1167	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_003384945.1	s__Clavibacter sp003384945	78.6728	422	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647635.1	s__Leifsonia xyli_A	78.6603	388	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	78.1278	396	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807485.1	s__Microbacterium sp016807485	78.0896	253	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	78.0201	371	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:41,094] [INFO] GTDB search result was written to GCF_004078635.1_ASM407863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:41,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:41,098] [INFO] DFAST_QC result json was written to GCF_004078635.1_ASM407863v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:41,098] [INFO] DFAST_QC completed!
[2024-01-24 12:30:41,098] [INFO] Total running time: 0h1m19s