[2024-01-24 13:18:26,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,319] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference
[2024-01-24 13:18:27,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,480] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg551e01a7-d918-4e83-a540-e5b6ba619f1f/GCF_000421845.1_ASM42184v1_genomic.fna.gz | prodigal -d GCF_000421845.1_ASM42184v1_genomic.fna/cds.fna -a GCF_000421845.1_ASM42184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:35,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:35,553] [INFO] Task started: HMMsearch
[2024-01-24 13:18:35,553] [INFO] Running command: hmmsearch --tblout GCF_000421845.1_ASM42184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference/reference_markers.hmm GCF_000421845.1_ASM42184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:35,731] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:35,732] [INFO] Found 6/6 markers.
[2024-01-24 13:18:35,755] [INFO] Query marker FASTA was written to GCF_000421845.1_ASM42184v1_genomic.fna/markers.fasta
[2024-01-24 13:18:35,756] [INFO] Task started: Blastn
[2024-01-24 13:18:35,756] [INFO] Running command: blastn -query GCF_000421845.1_ASM42184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference/reference_markers.fasta -out GCF_000421845.1_ASM42184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:36,865] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:36,873] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:36,873] [INFO] Target genome list was writen to GCF_000421845.1_ASM42184v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:36,878] [INFO] Task started: fastANI
[2024-01-24 13:18:36,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg551e01a7-d918-4e83-a540-e5b6ba619f1f/GCF_000421845.1_ASM42184v1_genomic.fna.gz --refList GCF_000421845.1_ASM42184v1_genomic.fna/target_genomes.txt --output GCF_000421845.1_ASM42184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:46,766] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:46,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:46,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:46,780] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:46,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:46,780] [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 chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	100.0	975	975	95	conclusive
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	88.7057	774	975	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	83.3111	646	975	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	83.0518	641	975	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	82.8905	572	975	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	82.5815	548	975	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	82.4842	567	975	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	82.2117	558	975	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	82.0953	600	975	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	81.155	484	975	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.4752	325	975	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4734	325	975	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.2302	358	975	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.9873	297	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:46,783] [INFO] DFAST Taxonomy check result was written to GCF_000421845.1_ASM42184v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:46,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:46,783] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:46,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference/checkm_data
[2024-01-24 13:18:46,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:46,828] [INFO] Task started: CheckM
[2024-01-24 13:18:46,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421845.1_ASM42184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421845.1_ASM42184v1_genomic.fna/checkm_input GCF_000421845.1_ASM42184v1_genomic.fna/checkm_result
[2024-01-24 13:19:15,969] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:15,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,987] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:15,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:15,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421845.1_ASM42184v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:15,988] [INFO] Task started: Blastn
[2024-01-24 13:19:15,988] [INFO] Running command: blastn -query GCF_000421845.1_ASM42184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b8ad48-ebd2-49d4-94a1-089c52ef6fe5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421845.1_ASM42184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,846] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:17,846] [INFO] Target genome list was writen to GCF_000421845.1_ASM42184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:17,863] [INFO] Task started: fastANI
[2024-01-24 13:19:17,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg551e01a7-d918-4e83-a540-e5b6ba619f1f/GCF_000421845.1_ASM42184v1_genomic.fna.gz --refList GCF_000421845.1_ASM42184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421845.1_ASM42184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:27,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:27,828] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:27,828] [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_000421845.1	s__Leucobacter chironomi	100.0	975	975	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	88.6967	773	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_003569785.1	s__Leucobacter sp003569785	83.486	618	975	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	83.293	648	975	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	82.8683	572	975	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	82.4817	567	975	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	82.371	574	975	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	82.2136	579	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_000980875.1	s__Leucobacter sp000980875	82.0377	550	975	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	81.8547	569	975	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	81.7416	551	975	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	81.6877	491	975	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 13:19:27,830] [INFO] GTDB search result was written to GCF_000421845.1_ASM42184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:27,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:27,834] [INFO] DFAST_QC result json was written to GCF_000421845.1_ASM42184v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:27,834] [INFO] DFAST_QC completed!
[2024-01-24 13:19:27,834] [INFO] Total running time: 0h1m2s