[2024-01-24 12:37:09,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,653] [INFO] DQC Reference Directory: /var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference
[2024-01-24 12:37:11,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,020] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,020] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7b6767e-1419-44a4-a4a0-c04096ac5b78/GCF_014204935.1_ASM1420493v1_genomic.fna.gz | prodigal -d GCF_014204935.1_ASM1420493v1_genomic.fna/cds.fna -a GCF_014204935.1_ASM1420493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:21,084] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:21,085] [INFO] Task started: HMMsearch
[2024-01-24 12:37:21,085] [INFO] Running command: hmmsearch --tblout GCF_014204935.1_ASM1420493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference/reference_markers.hmm GCF_014204935.1_ASM1420493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:21,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:21,363] [INFO] Found 6/6 markers.
[2024-01-24 12:37:21,395] [INFO] Query marker FASTA was written to GCF_014204935.1_ASM1420493v1_genomic.fna/markers.fasta
[2024-01-24 12:37:21,395] [INFO] Task started: Blastn
[2024-01-24 12:37:21,395] [INFO] Running command: blastn -query GCF_014204935.1_ASM1420493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference/reference_markers.fasta -out GCF_014204935.1_ASM1420493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:22,587] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:22,593] [INFO] Selected 21 target genomes.
[2024-01-24 12:37:22,593] [INFO] Target genome list was writen to GCF_014204935.1_ASM1420493v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:22,604] [INFO] Task started: fastANI
[2024-01-24 12:37:22,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7b6767e-1419-44a4-a4a0-c04096ac5b78/GCF_014204935.1_ASM1420493v1_genomic.fna.gz --refList GCF_014204935.1_ASM1420493v1_genomic.fna/target_genomes.txt --output GCF_014204935.1_ASM1420493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:36,664] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:36,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:36,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:36,685] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:36,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:36,686] [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 lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	100.0	1214	1214	95	conclusive
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	84.4687	787	1214	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	79.7141	467	1214	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.7	446	1214	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	79.6925	474	1214	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	79.593	452	1214	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.3269	472	1214	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	79.2797	429	1214	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.2691	467	1214	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.1976	479	1214	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.1676	482	1214	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.1268	466	1214	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.0985	415	1214	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.0701	478	1214	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.9699	460	1214	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.844	505	1214	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.7625	414	1214	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	78.7197	470	1214	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.477	393	1214	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.4232	450	1214	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.3049	461	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:36,687] [INFO] DFAST Taxonomy check result was written to GCF_014204935.1_ASM1420493v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:36,688] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:36,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:36,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference/checkm_data
[2024-01-24 12:37:36,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:36,731] [INFO] Task started: CheckM
[2024-01-24 12:37:36,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204935.1_ASM1420493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204935.1_ASM1420493v1_genomic.fna/checkm_input GCF_014204935.1_ASM1420493v1_genomic.fna/checkm_result
[2024-01-24 12:38:09,589] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:09,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:09,615] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:09,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:09,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204935.1_ASM1420493v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:09,617] [INFO] Task started: Blastn
[2024-01-24 12:38:09,617] [INFO] Running command: blastn -query GCF_014204935.1_ASM1420493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefad4f1d-00e3-47df-9a5b-8a65f039bd23/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204935.1_ASM1420493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:11,585] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:11,589] [INFO] Selected 15 target genomes.
[2024-01-24 12:38:11,589] [INFO] Target genome list was writen to GCF_014204935.1_ASM1420493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:11,604] [INFO] Task started: fastANI
[2024-01-24 12:38:11,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7b6767e-1419-44a4-a4a0-c04096ac5b78/GCF_014204935.1_ASM1420493v1_genomic.fna.gz --refList GCF_014204935.1_ASM1420493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204935.1_ASM1420493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:22,258] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:22,274] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:22,275] [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_014204935.1	s__Conyzicola lurida	100.0	1213	1214	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_014639655.1	s__Conyzicola nivalis	84.4586	788	1214	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	80.9753	575	1214	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	80.5402	529	1214	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	80.5209	420	1214	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	80.0839	482	1214	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	79.7728	481	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057645.1	s__Marisediminicola senii	79.7427	464	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.4792	518	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	79.3704	441	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907085.1	s__Clavibacter michiganensis_O	79.201	476	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240635.1	s__Clavibacter tessellarius	79.1475	480	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	-
GCF_900142065.1	s__Agromyces cerinus	79.14	475	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898805.1	s__Leifsonia sp001898805	78.7994	474	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	78.7924	465	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:22,276] [INFO] GTDB search result was written to GCF_014204935.1_ASM1420493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:22,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:22,282] [INFO] DFAST_QC result json was written to GCF_014204935.1_ASM1420493v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:22,282] [INFO] DFAST_QC completed!
[2024-01-24 12:38:22,282] [INFO] Total running time: 0h1m13s