[2024-01-24 15:10:19,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference
[2024-01-24 15:10:22,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,719] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stga07961a1-b690-4dd1-8b8f-2df94723a2ff/GCF_018304965.1_ASM1830496v1_genomic.fna.gz | prodigal -d GCF_018304965.1_ASM1830496v1_genomic.fna/cds.fna -a GCF_018304965.1_ASM1830496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:37,630] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:37,631] [INFO] Task started: HMMsearch
[2024-01-24 15:10:37,631] [INFO] Running command: hmmsearch --tblout GCF_018304965.1_ASM1830496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference/reference_markers.hmm GCF_018304965.1_ASM1830496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:37,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:37,916] [INFO] Found 6/6 markers.
[2024-01-24 15:10:37,959] [INFO] Query marker FASTA was written to GCF_018304965.1_ASM1830496v1_genomic.fna/markers.fasta
[2024-01-24 15:10:37,960] [INFO] Task started: Blastn
[2024-01-24 15:10:37,960] [INFO] Running command: blastn -query GCF_018304965.1_ASM1830496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference/reference_markers.fasta -out GCF_018304965.1_ASM1830496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:38,838] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:38,842] [INFO] Selected 11 target genomes.
[2024-01-24 15:10:38,842] [INFO] Target genome list was writen to GCF_018304965.1_ASM1830496v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:38,847] [INFO] Task started: fastANI
[2024-01-24 15:10:38,847] [INFO] Running command: fastANI --query /var/lib/cwl/stga07961a1-b690-4dd1-8b8f-2df94723a2ff/GCF_018304965.1_ASM1830496v1_genomic.fna.gz --refList GCF_018304965.1_ASM1830496v1_genomic.fna/target_genomes.txt --output GCF_018304965.1_ASM1830496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:51,116] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:51,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:51,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:51,126] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:51,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:51,127] [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
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	100.0	1533	1534	95	conclusive
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	87.0844	1058	1534	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	85.8157	1067	1534	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	84.2617	1073	1534	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	83.9212	1045	1534	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	83.1328	962	1534	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.3403	451	1534	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	78.3871	408	1534	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	78.3404	348	1534	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	78.2547	347	1534	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	78.1547	314	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:51,128] [INFO] DFAST Taxonomy check result was written to GCF_018304965.1_ASM1830496v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:51,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:51,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:51,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference/checkm_data
[2024-01-24 15:10:51,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:51,179] [INFO] Task started: CheckM
[2024-01-24 15:10:51,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018304965.1_ASM1830496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018304965.1_ASM1830496v1_genomic.fna/checkm_input GCF_018304965.1_ASM1830496v1_genomic.fna/checkm_result
[2024-01-24 15:11:38,125] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:38,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:38,158] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:38,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:38,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018304965.1_ASM1830496v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:38,159] [INFO] Task started: Blastn
[2024-01-24 15:11:38,159] [INFO] Running command: blastn -query GCF_018304965.1_ASM1830496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83fe6e38-837a-4c45-8a37-ea066ab5d35a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018304965.1_ASM1830496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:39,710] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:39,714] [INFO] Selected 6 target genomes.
[2024-01-24 15:11:39,714] [INFO] Target genome list was writen to GCF_018304965.1_ASM1830496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:39,719] [INFO] Task started: fastANI
[2024-01-24 15:11:39,719] [INFO] Running command: fastANI --query /var/lib/cwl/stga07961a1-b690-4dd1-8b8f-2df94723a2ff/GCF_018304965.1_ASM1830496v1_genomic.fna.gz --refList GCF_018304965.1_ASM1830496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018304965.1_ASM1830496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:48,424] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:48,431] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:48,431] [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_018304965.1	s__Collimonas antrihumi	100.0	1533	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107095.1	s__Collimonas sp900107095	91.9759	1146	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111995.1	s__Collimonas sp900111995	91.5993	1177	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113705.1	s__Collimonas sp900113705	91.5572	1231	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018305005.1	s__Collimonas sp018305005	87.0746	1059	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564105.1	s__Collimonas sp002564105	84.2332	1084	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:48,446] [INFO] GTDB search result was written to GCF_018304965.1_ASM1830496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:48,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:48,456] [INFO] DFAST_QC result json was written to GCF_018304965.1_ASM1830496v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:48,457] [INFO] DFAST_QC completed!
[2024-01-24 15:11:48,457] [INFO] Total running time: 0h1m29s