[2024-01-24 11:20:04,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference
[2024-01-24 11:20:05,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,501] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,501] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f6ad9a-d5f9-4e89-bccc-bbae266ecd85/GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/cds.fna -a GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:15,023] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:15,023] [INFO] Task started: HMMsearch
[2024-01-24 11:20:15,023] [INFO] Running command: hmmsearch --tblout GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference/reference_markers.hmm GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:15,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:15,221] [INFO] Found 6/6 markers.
[2024-01-24 11:20:15,248] [INFO] Query marker FASTA was written to GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:20:15,248] [INFO] Task started: Blastn
[2024-01-24 11:20:15,248] [INFO] Running command: blastn -query GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference/reference_markers.fasta -out GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:16,194] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:16,197] [INFO] Selected 14 target genomes.
[2024-01-24 11:20:16,197] [INFO] Target genome list was writen to GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:20:16,223] [INFO] Task started: fastANI
[2024-01-24 11:20:16,223] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f6ad9a-d5f9-4e89-bccc-bbae266ecd85/GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna.gz --refList GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:25,205] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:25,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:25,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:25,217] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:25,217] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:25,218] [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
Mycetocola miduiensis	strain=CGMCC 1.11101	GCA_900115155.1	995034	995034	type	True	100.0	1093	1094	95	conclusive
Mycetocola manganoxydans	strain=KCTC 19753	GCA_014651755.1	699879	699879	type	True	81.9923	624	1094	95	below_threshold
Mycetocola manganoxydans	strain=CCTCC AB209002	GCA_003667545.1	699879	699879	type	True	81.9698	625	1094	95	below_threshold
Mycetocola zhujimingii	strain=449 = CGMCC 1.16372	GCA_003065425.1	2079792	2079792	type	True	80.6014	493	1094	95	below_threshold
Mycetocola zhadangensis	strain=CGMCC 1.12042	GCA_014636455.1	1164595	1164595	type	True	80.2021	459	1094	95	below_threshold
Mycetocola zhadangensis	strain=ZD1-4	GCA_003668565.1	1164595	1164595	type	True	80.1192	469	1094	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.8435	333	1094	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	78.4455	306	1094	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.374	305	1094	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	78.1568	265	1094	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.0883	309	1094	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	78.0631	247	1094	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.0581	258	1094	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.7901	237	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:25,220] [INFO] DFAST Taxonomy check result was written to GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:20:25,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:25,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:25,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference/checkm_data
[2024-01-24 11:20:25,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:25,253] [INFO] Task started: CheckM
[2024-01-24 11:20:25,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/checkm_input GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:20:56,293] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:56,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,310] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:56,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:56,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:20:56,311] [INFO] Task started: Blastn
[2024-01-24 11:20:56,311] [INFO] Running command: blastn -query GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg25441285-a247-4f0c-a2bd-16d3cd0b487e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:57,708] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:57,711] [INFO] Selected 8 target genomes.
[2024-01-24 11:20:57,711] [INFO] Target genome list was writen to GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:57,746] [INFO] Task started: fastANI
[2024-01-24 11:20:57,746] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f6ad9a-d5f9-4e89-bccc-bbae266ecd85/GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna.gz --refList GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:03,411] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:03,419] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:03,419] [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_900115155.1	s__Mycetocola_A miduiensis	100.0	1093	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003667545.1	s__Mycetocola_A manganoxydans	81.9579	626	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015752285.1	s__Mycetocola_A sp015752285	81.6932	589	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065425.1	s__Mycetocola_A zhujimingii	80.6023	494	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	98.22	98.22	0.95	0.95	2	-
GCF_003668565.1	s__Mycetocola_A zhadangensis	80.1158	470	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900167575.1	s__Okibacterium fritillariae	78.8437	333	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078635.1	s__Labedella phragmitis	78.451	305	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425325.1	s__Leifsonia_A sp001425325	78.4161	319	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:03,420] [INFO] GTDB search result was written to GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:03,421] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:03,424] [INFO] DFAST_QC result json was written to GCF_900115155.1_IMG-taxon_2667527394_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:21:03,424] [INFO] DFAST_QC completed!
[2024-01-24 11:21:03,424] [INFO] Total running time: 0h0m59s