[2024-01-24 13:58:11,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,122] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,122] [INFO] DQC Reference Directory: /var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference
[2024-01-24 13:58:12,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,464] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,465] [INFO] Running command: gunzip -c /var/lib/cwl/stg819ad539-7979-4fc6-97bb-a6049c1f360c/GCF_014639655.1_ASM1463965v1_genomic.fna.gz | prodigal -d GCF_014639655.1_ASM1463965v1_genomic.fna/cds.fna -a GCF_014639655.1_ASM1463965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:22,622] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:22,622] [INFO] Task started: HMMsearch
[2024-01-24 13:58:22,623] [INFO] Running command: hmmsearch --tblout GCF_014639655.1_ASM1463965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference/reference_markers.hmm GCF_014639655.1_ASM1463965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:22,927] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:22,928] [INFO] Found 6/6 markers.
[2024-01-24 13:58:22,959] [INFO] Query marker FASTA was written to GCF_014639655.1_ASM1463965v1_genomic.fna/markers.fasta
[2024-01-24 13:58:22,960] [INFO] Task started: Blastn
[2024-01-24 13:58:22,960] [INFO] Running command: blastn -query GCF_014639655.1_ASM1463965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference/reference_markers.fasta -out GCF_014639655.1_ASM1463965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,077] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,081] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:24,081] [INFO] Target genome list was writen to GCF_014639655.1_ASM1463965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,090] [INFO] Task started: fastANI
[2024-01-24 13:58:24,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg819ad539-7979-4fc6-97bb-a6049c1f360c/GCF_014639655.1_ASM1463965v1_genomic.fna.gz --refList GCF_014639655.1_ASM1463965v1_genomic.fna/target_genomes.txt --output GCF_014639655.1_ASM1463965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:38,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:38,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:38,238] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:38,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:38,238] [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
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	100.0	1111	1111	95	conclusive
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	84.4245	806	1111	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	79.6326	454	1111	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.4345	433	1111	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	79.3683	397	1111	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.2943	428	1111	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	79.2655	417	1111	95	below_threshold
Marisediminicola antarctica	strain=ZS314	GCA_009930795.1	674079	674079	type	True	79.2131	427	1111	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.2079	421	1111	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.1457	437	1111	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.1361	450	1111	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.1131	379	1111	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.1074	429	1111	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	79.0215	442	1111	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	78.9323	406	1111	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	78.9218	424	1111	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.5997	402	1111	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	78.5785	397	1111	95	below_threshold
Salinibacterium xinjiangense	strain=CGMCC 1.5381	GCA_014645015.1	386302	386302	type	True	78.4553	330	1111	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.4525	418	1111	95	below_threshold
Salinibacterium xinjiangense	strain=CGMCC 1.05381	GCA_900230175.1	386302	386302	type	True	78.3823	335	1111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,246] [INFO] DFAST Taxonomy check result was written to GCF_014639655.1_ASM1463965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:38,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:38,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:38,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference/checkm_data
[2024-01-24 13:58:38,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:38,290] [INFO] Task started: CheckM
[2024-01-24 13:58:38,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639655.1_ASM1463965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639655.1_ASM1463965v1_genomic.fna/checkm_input GCF_014639655.1_ASM1463965v1_genomic.fna/checkm_result
[2024-01-24 13:59:11,927] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:11,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,951] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:11,951] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:11,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639655.1_ASM1463965v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:11,952] [INFO] Task started: Blastn
[2024-01-24 13:59:11,952] [INFO] Running command: blastn -query GCF_014639655.1_ASM1463965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc86a4ca5-9d63-43ab-8f77-26350a38ff10/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639655.1_ASM1463965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:13,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:13,806] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:13,807] [INFO] Target genome list was writen to GCF_014639655.1_ASM1463965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:13,833] [INFO] Task started: fastANI
[2024-01-24 13:59:13,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg819ad539-7979-4fc6-97bb-a6049c1f360c/GCF_014639655.1_ASM1463965v1_genomic.fna.gz --refList GCF_014639655.1_ASM1463965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639655.1_ASM1463965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:25,006] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:25,032] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:25,032] [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_014639655.1	s__Conyzicola nivalis	100.0	1111	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014204935.1	s__Conyzicola lurida	84.4495	804	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310685.1	s__Conyzicola arctica	80.9565	526	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725325.1	s__Rhodoglobus sp001725325	80.4017	513	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_013297645.1	s__JAAFHU01 sp013297645	80.3477	397	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAAFHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920435.1	s__Rhodoglobus sp903920435	80.0429	458	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_018449675.1	s__Glaciihabitans sp018449675	79.5664	461	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.4008	487	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	79.1381	377	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	79.1029	438	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	79.0971	430	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217685.1	s__Lacisediminihabitans sp014217685	79.0243	387	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749405.1	s__Agromyces lapidis	78.9848	407	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003265.1	s__Glaciihabitans tibetensis	78.9211	407	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003367665.1	s__Leifsonia sp003367665	78.7625	433	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664105.1	s__Leifsonia sp003664105	78.6809	395	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,034] [INFO] GTDB search result was written to GCF_014639655.1_ASM1463965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:25,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:25,039] [INFO] DFAST_QC result json was written to GCF_014639655.1_ASM1463965v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:25,039] [INFO] DFAST_QC completed!
[2024-01-24 13:59:25,039] [INFO] Total running time: 0h1m14s