[2024-01-24 11:44:05,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference
[2024-01-24 11:44:08,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,842] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,842] [INFO] Running command: gunzip -c /var/lib/cwl/stge3b07970-f0ea-48f4-ae05-7c72fabf7ca3/GCF_014396385.1_ASM1439638v1_genomic.fna.gz | prodigal -d GCF_014396385.1_ASM1439638v1_genomic.fna/cds.fna -a GCF_014396385.1_ASM1439638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:16,467] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:16,467] [INFO] Task started: HMMsearch
[2024-01-24 11:44:16,468] [INFO] Running command: hmmsearch --tblout GCF_014396385.1_ASM1439638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference/reference_markers.hmm GCF_014396385.1_ASM1439638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:16,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:16,688] [INFO] Found 6/6 markers.
[2024-01-24 11:44:16,714] [INFO] Query marker FASTA was written to GCF_014396385.1_ASM1439638v1_genomic.fna/markers.fasta
[2024-01-24 11:44:16,714] [INFO] Task started: Blastn
[2024-01-24 11:44:16,714] [INFO] Running command: blastn -query GCF_014396385.1_ASM1439638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference/reference_markers.fasta -out GCF_014396385.1_ASM1439638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:17,403] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:17,408] [INFO] Selected 16 target genomes.
[2024-01-24 11:44:17,408] [INFO] Target genome list was writen to GCF_014396385.1_ASM1439638v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:17,535] [INFO] Task started: fastANI
[2024-01-24 11:44:17,536] [INFO] Running command: fastANI --query /var/lib/cwl/stge3b07970-f0ea-48f4-ae05-7c72fabf7ca3/GCF_014396385.1_ASM1439638v1_genomic.fna.gz --refList GCF_014396385.1_ASM1439638v1_genomic.fna/target_genomes.txt --output GCF_014396385.1_ASM1439638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:26,692] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:26,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:26,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:26,704] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:26,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:26,705] [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 denitrificans	strain=KACC 14055	GCA_014396385.1	683042	683042	type	True	100.0	801	801	95	conclusive
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	79.1134	281	801	95	below_threshold
Leucobacter aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	79.0662	269	801	95	below_threshold
Leucobacter aridicollis	strain=L-9	GCA_016758215.1	283878	283878	type	True	79.0083	265	801	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	78.6423	238	801	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	78.5773	217	801	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	78.4502	234	801	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	78.3083	208	801	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	78.1265	233	801	95	below_threshold
Leucobacter exalbidus	strain=DSM 22850	GCA_017834145.1	662960	662960	type	True	78.0048	180	801	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	77.6671	184	801	95	below_threshold
Leucobacter weissii	strain=S27	GCA_017565745.1	1983706	1983706	type	True	77.4703	148	801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:26,706] [INFO] DFAST Taxonomy check result was written to GCF_014396385.1_ASM1439638v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:26,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:26,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:26,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference/checkm_data
[2024-01-24 11:44:26,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:26,740] [INFO] Task started: CheckM
[2024-01-24 11:44:26,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014396385.1_ASM1439638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014396385.1_ASM1439638v1_genomic.fna/checkm_input GCF_014396385.1_ASM1439638v1_genomic.fna/checkm_result
[2024-01-24 11:44:54,078] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:54,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,094] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:54,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:54,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014396385.1_ASM1439638v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:54,095] [INFO] Task started: Blastn
[2024-01-24 11:44:54,096] [INFO] Running command: blastn -query GCF_014396385.1_ASM1439638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d4531cf-bc47-4384-96a2-3140a68273d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014396385.1_ASM1439638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:55,050] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:55,054] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:55,054] [INFO] Target genome list was writen to GCF_014396385.1_ASM1439638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:55,067] [INFO] Task started: fastANI
[2024-01-24 11:44:55,067] [INFO] Running command: fastANI --query /var/lib/cwl/stge3b07970-f0ea-48f4-ae05-7c72fabf7ca3/GCF_014396385.1_ASM1439638v1_genomic.fna.gz --refList GCF_014396385.1_ASM1439638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014396385.1_ASM1439638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:06,284] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:06,302] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:06,303] [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_014396385.1	s__Leucobacter denitrificans	100.0	801	801	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_006716085.1	s__Leucobacter komagatae	79.0542	280	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409595.1	s__Leucobacter aridicollis	78.9956	268	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.50	96.99	0.93	0.86	3	-
GCF_004208635.1	s__Leucobacter triazinivorans	78.7108	239	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482305.1	s__Leucobacter sp001482305	78.6651	262	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421845.1	s__Leucobacter chironomi	78.6302	219	801	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	78.5519	190	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	78.4778	232	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	78.3712	212	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758255.1	s__Leucobacter chromiireducens	78.1989	207	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522535.1	s__Leucobacter sp016522535	78.1912	203	801	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	78.1635	237	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990305.1	s__Leucobacter sp017990305	78.1284	155	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014530035.1	s__Leucobacter sp014530035	78.068	156	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003569785.1	s__Leucobacter sp003569785	78.0619	208	801	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	78.0281	211	801	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 11:45:06,304] [INFO] GTDB search result was written to GCF_014396385.1_ASM1439638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:06,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:06,308] [INFO] DFAST_QC result json was written to GCF_014396385.1_ASM1439638v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:06,308] [INFO] DFAST_QC completed!
[2024-01-24 11:45:06,309] [INFO] Total running time: 0h1m1s