[2024-01-25 19:44:21,497] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:21,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:21,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference
[2024-01-25 19:44:22,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:22,608] [INFO] Task started: Prodigal
[2024-01-25 19:44:22,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg9423d104-12fd-48bb-b54c-82819adcd4d3/GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/cds.fna -a GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:30,625] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:30,625] [INFO] Task started: HMMsearch
[2024-01-25 19:44:30,625] [INFO] Running command: hmmsearch --tblout GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference/reference_markers.hmm GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:30,824] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:30,825] [INFO] Found 6/6 markers.
[2024-01-25 19:44:30,852] [INFO] Query marker FASTA was written to GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:44:30,852] [INFO] Task started: Blastn
[2024-01-25 19:44:30,852] [INFO] Running command: blastn -query GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference/reference_markers.fasta -out GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:31,391] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:31,394] [INFO] Selected 17 target genomes.
[2024-01-25 19:44:31,394] [INFO] Target genome list was writen to GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:44:31,402] [INFO] Task started: fastANI
[2024-01-25 19:44:31,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg9423d104-12fd-48bb-b54c-82819adcd4d3/GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna.gz --refList GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:44,142] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:44,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:44,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:44,149] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:44,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:44,149] [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 thermohalophilus	strain=DSM 45514	GCA_900102685.1	1236220	1236220	type	True	100.0	1040	1043	95	conclusive
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	77.6819	200	1043	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_900156615.1	714067	714067	type	True	77.5969	197	1043	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	77.5364	298	1043	95	below_threshold
Kroppenstedtia guangzhouensis	strain=CGMCC 1.12404	GCA_014637345.1	1274356	1274356	type	True	77.2226	190	1043	95	below_threshold
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	76.8319	145	1043	95	below_threshold
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	76.693	91	1043	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.431	92	1043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:44,151] [INFO] DFAST Taxonomy check result was written to GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:44:44,151] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:44,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:44,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference/checkm_data
[2024-01-25 19:44:44,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:44,185] [INFO] Task started: CheckM
[2024-01-25 19:44:44,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/checkm_input GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:45:11,175] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:11,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:11,205] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:11,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:11,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:45:11,206] [INFO] Task started: Blastn
[2024-01-25 19:45:11,206] [INFO] Running command: blastn -query GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8467a5b4-5f6d-42d6-9a53-a32f106c3f7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:11,984] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:11,986] [INFO] Selected 18 target genomes.
[2024-01-25 19:45:11,986] [INFO] Target genome list was writen to GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:12,015] [INFO] Task started: fastANI
[2024-01-25 19:45:12,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg9423d104-12fd-48bb-b54c-82819adcd4d3/GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna.gz --refList GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:24,480] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:24,489] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:24,489] [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_900102685.1	s__Melghirimyces thermohalophilus	100.0	1040	1043	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	77.6819	200	1043	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	77.5252	299	1043	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_014637345.1	s__Kroppenstedtia guangzhouensis	77.2226	190	1043	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_002245355.1	s__Paludifilum halophilum	76.8547	146	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Paludifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013265585.1	s__Kroppenstedtia_A pulmonis	76.6916	90	1043	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	-
GCF_003001905.1	s__Planifilum fimeticola	76.431	92	1043	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:24,490] [INFO] GTDB search result was written to GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:24,491] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:24,493] [INFO] DFAST_QC result json was written to GCF_900102685.1_IMG-taxon_2615840705_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:45:24,493] [INFO] DFAST_QC completed!
[2024-01-25 19:45:24,493] [INFO] Total running time: 0h1m3s