[2024-01-24 12:14:34,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference
[2024-01-24 12:14:35,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,397] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ec17eda-4398-4830-8c58-6b87a71b20b8/GCF_017565705.1_ASM1756570v1_genomic.fna.gz | prodigal -d GCF_017565705.1_ASM1756570v1_genomic.fna/cds.fna -a GCF_017565705.1_ASM1756570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,159] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,159] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,159] [INFO] Running command: hmmsearch --tblout GCF_017565705.1_ASM1756570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference/reference_markers.hmm GCF_017565705.1_ASM1756570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:43,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:43,447] [INFO] Found 6/6 markers.
[2024-01-24 12:14:43,480] [INFO] Query marker FASTA was written to GCF_017565705.1_ASM1756570v1_genomic.fna/markers.fasta
[2024-01-24 12:14:43,480] [INFO] Task started: Blastn
[2024-01-24 12:14:43,480] [INFO] Running command: blastn -query GCF_017565705.1_ASM1756570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference/reference_markers.fasta -out GCF_017565705.1_ASM1756570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:44,592] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:44,605] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:44,605] [INFO] Target genome list was writen to GCF_017565705.1_ASM1756570v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:44,642] [INFO] Task started: fastANI
[2024-01-24 12:14:44,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ec17eda-4398-4830-8c58-6b87a71b20b8/GCF_017565705.1_ASM1756570v1_genomic.fna.gz --refList GCF_017565705.1_ASM1756570v1_genomic.fna/target_genomes.txt --output GCF_017565705.1_ASM1756570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:54,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:54,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:54,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:54,578] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:54,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:54,578] [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 ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	100.0	1068	1072	95	conclusive
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	83.3141	590	1072	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	82.8962	565	1072	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	82.7426	610	1072	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	82.0299	583	1072	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	81.981	514	1072	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	81.8426	523	1072	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	81.8401	572	1072	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	81.8301	512	1072	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	81.2689	433	1072	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.3967	326	1072	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	78.3684	317	1072	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3572	386	1072	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.2721	291	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:54,579] [INFO] DFAST Taxonomy check result was written to GCF_017565705.1_ASM1756570v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:54,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:54,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:54,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference/checkm_data
[2024-01-24 12:14:54,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:54,614] [INFO] Task started: CheckM
[2024-01-24 12:14:54,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017565705.1_ASM1756570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017565705.1_ASM1756570v1_genomic.fna/checkm_input GCF_017565705.1_ASM1756570v1_genomic.fna/checkm_result
[2024-01-24 12:15:23,243] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:23,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,259] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:23,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:23,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017565705.1_ASM1756570v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:23,259] [INFO] Task started: Blastn
[2024-01-24 12:15:23,259] [INFO] Running command: blastn -query GCF_017565705.1_ASM1756570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c1e07a1-880e-4275-a008-6c86f32f342f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017565705.1_ASM1756570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:24,964] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:24,967] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:24,967] [INFO] Target genome list was writen to GCF_017565705.1_ASM1756570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:24,975] [INFO] Task started: fastANI
[2024-01-24 12:15:24,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ec17eda-4398-4830-8c58-6b87a71b20b8/GCF_017565705.1_ASM1756570v1_genomic.fna.gz --refList GCF_017565705.1_ASM1756570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017565705.1_ASM1756570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:34,745] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:34,754] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:34,755] [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_017565705.1	s__Leucobacter ruminantium	100.0	1068	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004028235.1	s__Leucobacter muris	83.3692	585	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_000421845.1	s__Leucobacter chironomi	82.911	564	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273835.1	s__Leucobacter celer	82.7374	610	1072	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	82.7162	553	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982315.1	s__Leucobacter massiliensis	82.0245	511	1072	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	81.8268	486	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633415.1	s__Leucobacter sp000633415	81.8235	515	1072	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	81.8148	525	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_016522535.1	s__Leucobacter sp016522535	81.505	453	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477055.1	s__Leucobacter chromiiresistens_A	81.4814	478	1072	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	81.4364	514	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	81.3699	506	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336855.1	s__Leucobacter sp002336855	79.1608	348	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,756] [INFO] GTDB search result was written to GCF_017565705.1_ASM1756570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:34,756] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:34,759] [INFO] DFAST_QC result json was written to GCF_017565705.1_ASM1756570v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:34,759] [INFO] DFAST_QC completed!
[2024-01-24 12:15:34,759] [INFO] Total running time: 0h1m1s