[2024-01-24 15:27:41,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference
[2024-01-24 15:27:43,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,882] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg97d3a628-0458-49e9-b460-add7598ce2a1/GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/cds.fna -a GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:55,631] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:55,631] [INFO] Task started: HMMsearch
[2024-01-24 15:27:55,632] [INFO] Running command: hmmsearch --tblout GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference/reference_markers.hmm GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:55,892] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:55,894] [INFO] Found 6/6 markers.
[2024-01-24 15:27:55,931] [INFO] Query marker FASTA was written to GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:27:55,931] [INFO] Task started: Blastn
[2024-01-24 15:27:55,932] [INFO] Running command: blastn -query GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference/reference_markers.fasta -out GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:56,528] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:56,532] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:56,532] [INFO] Target genome list was writen to GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:27:56,566] [INFO] Task started: fastANI
[2024-01-24 15:27:56,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d3a628-0458-49e9-b460-add7598ce2a1/GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna.gz --refList GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:03,974] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:03,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:03,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:03,987] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:03,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:03,988] [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
Melghirimyces algeriensis	strain=DSM 45474	GCA_900182565.1	910412	910412	type	True	100.0	1127	1128	95	conclusive
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	77.4771	129	1128	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	77.4289	169	1128	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_900156615.1	714067	714067	type	True	77.3652	135	1128	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	77.1415	84	1128	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.9704	86	1128	95	below_threshold
Kroppenstedtia guangzhouensis	strain=CGMCC 1.12404	GCA_014637345.1	1274356	1274356	type	True	76.939	159	1128	95	below_threshold
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	76.6347	101	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:03,990] [INFO] DFAST Taxonomy check result was written to GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:28:03,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:03,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:03,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference/checkm_data
[2024-01-24 15:28:03,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:04,032] [INFO] Task started: CheckM
[2024-01-24 15:28:04,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/checkm_input GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:28:44,189] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:44,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:44,212] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:44,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:44,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:28:44,213] [INFO] Task started: Blastn
[2024-01-24 15:28:44,213] [INFO] Running command: blastn -query GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg90463cd0-3386-49f6-b967-9bf2d77d1c23/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:44,997] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:45,007] [INFO] Selected 15 target genomes.
[2024-01-24 15:28:45,007] [INFO] Target genome list was writen to GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:45,023] [INFO] Task started: fastANI
[2024-01-24 15:28:45,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d3a628-0458-49e9-b460-add7598ce2a1/GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna.gz --refList GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:54,114] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:54,126] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:54,127] [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_900182565.1	s__Melghirimyces algeriensis	100.0	1127	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013282215.1	s__Kroppenstedtia eburnea	77.4771	129	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	99.43	98.85	0.98	0.95	3	-
GCF_003054245.1	s__Melghirimyces profundicolus	77.4289	169	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641195.1	s__Marinithermofilum abyssi	77.1415	84	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marinithermofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046315.1	s__Desmospora activa	76.9704	86	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Desmospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637345.1	s__Kroppenstedtia guangzhouensis	76.939	159	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013265585.1	s__Kroppenstedtia_A pulmonis	76.6331	101	1128	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:54,129] [INFO] GTDB search result was written to GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:54,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:54,133] [INFO] DFAST_QC result json was written to GCF_900182565.1_IMG-taxon_2724679802_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:28:54,133] [INFO] DFAST_QC completed!
[2024-01-24 15:28:54,133] [INFO] Total running time: 0h1m13s