[2024-01-24 11:52:04,670] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference
[2024-01-24 11:52:05,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,871] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg94e829ea-2f25-451b-bb24-68d4c684bf06/GCF_004028235.1_ASM402823v1_genomic.fna.gz | prodigal -d GCF_004028235.1_ASM402823v1_genomic.fna/cds.fna -a GCF_004028235.1_ASM402823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:14,702] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:14,703] [INFO] Task started: HMMsearch
[2024-01-24 11:52:14,703] [INFO] Running command: hmmsearch --tblout GCF_004028235.1_ASM402823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference/reference_markers.hmm GCF_004028235.1_ASM402823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:14,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:14,952] [INFO] Found 6/6 markers.
[2024-01-24 11:52:14,981] [INFO] Query marker FASTA was written to GCF_004028235.1_ASM402823v1_genomic.fna/markers.fasta
[2024-01-24 11:52:14,981] [INFO] Task started: Blastn
[2024-01-24 11:52:14,981] [INFO] Running command: blastn -query GCF_004028235.1_ASM402823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference/reference_markers.fasta -out GCF_004028235.1_ASM402823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:16,076] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:16,081] [INFO] Selected 20 target genomes.
[2024-01-24 11:52:16,081] [INFO] Target genome list was writen to GCF_004028235.1_ASM402823v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:16,108] [INFO] Task started: fastANI
[2024-01-24 11:52:16,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e829ea-2f25-451b-bb24-68d4c684bf06/GCF_004028235.1_ASM402823v1_genomic.fna.gz --refList GCF_004028235.1_ASM402823v1_genomic.fna/target_genomes.txt --output GCF_004028235.1_ASM402823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:29,131] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:29,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:29,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:29,149] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:29,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:29,150] [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 muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	100.0	1065	1070	95	conclusive
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	88.6643	774	1070	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	83.6564	688	1070	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	83.1819	579	1070	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	83.1769	672	1070	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	82.5024	581	1070	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	82.1774	603	1070	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	82.1454	586	1070	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	81.9773	582	1070	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	81.3004	454	1070	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	80.1587	480	1070	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.4481	391	1070	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4139	349	1070	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	78.1343	336	1070	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	78.1162	312	1070	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_900177335.1	1049583	1049583	type	True	77.1993	116	1070	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	77.1796	117	1070	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	77.084	116	1070	95	below_threshold
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	76.9435	155	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,152] [INFO] DFAST Taxonomy check result was written to GCF_004028235.1_ASM402823v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:29,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:29,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:29,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference/checkm_data
[2024-01-24 11:52:29,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:29,192] [INFO] Task started: CheckM
[2024-01-24 11:52:29,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004028235.1_ASM402823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004028235.1_ASM402823v1_genomic.fna/checkm_input GCF_004028235.1_ASM402823v1_genomic.fna/checkm_result
[2024-01-24 11:53:02,257] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:02,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:02,286] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:02,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:02,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004028235.1_ASM402823v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:02,287] [INFO] Task started: Blastn
[2024-01-24 11:53:02,287] [INFO] Running command: blastn -query GCF_004028235.1_ASM402823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056dadc2-7c98-40a1-91b7-7b5c62e6aa75/dqc_reference/reference_markers_gtdb.fasta -out GCF_004028235.1_ASM402823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:04,158] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:04,162] [INFO] Selected 16 target genomes.
[2024-01-24 11:53:04,162] [INFO] Target genome list was writen to GCF_004028235.1_ASM402823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:04,175] [INFO] Task started: fastANI
[2024-01-24 11:53:04,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e829ea-2f25-451b-bb24-68d4c684bf06/GCF_004028235.1_ASM402823v1_genomic.fna.gz --refList GCF_004028235.1_ASM402823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004028235.1_ASM402823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:15,788] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:15,805] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:15,806] [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_004028235.1	s__Leucobacter muris	100.0	1065	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	conclusive
GCF_000421845.1	s__Leucobacter chironomi	88.6603	774	1070	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	83.8167	639	1070	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	83.6556	688	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208635.1	s__Leucobacter triazinivorans	83.1995	669	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	83.197	577	1070	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	82.5176	579	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758175.1	s__Leucobacter zeae	82.2475	621	1070	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	82.0952	607	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	82.0368	565	1070	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	81.9257	547	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752355.1	s__Leucobacter sp002752355	81.7462	562	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_016522535.1	s__Leucobacter sp016522535	81.4939	503	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014652975.1	s__Kocuria marina	77.0134	121	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	-
GCF_006539885.1	s__Kocuria varians	76.9435	155	1070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:15,807] [INFO] GTDB search result was written to GCF_004028235.1_ASM402823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:15,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:15,812] [INFO] DFAST_QC result json was written to GCF_004028235.1_ASM402823v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:15,812] [INFO] DFAST_QC completed!
[2024-01-24 11:53:15,812] [INFO] Total running time: 0h1m11s