[2024-01-25 19:56:50,397] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:50,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:50,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference
[2024-01-25 19:56:51,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:51,575] [INFO] Task started: Prodigal
[2024-01-25 19:56:51,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg277d9504-9c65-470f-8de2-5fbc4422887b/GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/cds.fna -a GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:00,700] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:00,700] [INFO] Task started: HMMsearch
[2024-01-25 19:57:00,701] [INFO] Running command: hmmsearch --tblout GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference/reference_markers.hmm GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:00,923] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:00,924] [INFO] Found 6/6 markers.
[2024-01-25 19:57:00,952] [INFO] Query marker FASTA was written to GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:57:00,952] [INFO] Task started: Blastn
[2024-01-25 19:57:00,952] [INFO] Running command: blastn -query GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference/reference_markers.fasta -out GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:01,490] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:01,493] [INFO] Selected 17 target genomes.
[2024-01-25 19:57:01,493] [INFO] Target genome list was writen to GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:57:01,502] [INFO] Task started: fastANI
[2024-01-25 19:57:01,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg277d9504-9c65-470f-8de2-5fbc4422887b/GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna.gz --refList GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:13,442] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:13,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:13,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:13,448] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:13,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:13,448] [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
Marininema halotolerans	strain=DSM 45789	GCA_900116235.1	1155944	1155944	type	True	100.0	1175	1177	95	conclusive
Marininema mesophilum	strain=DSM 45610	GCA_900106775.1	1048340	1048340	type	True	79.2819	442	1177	95	below_threshold
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	76.6464	54	1177	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.4798	67	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:13,449] [INFO] DFAST Taxonomy check result was written to GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:57:13,450] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:13,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:13,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference/checkm_data
[2024-01-25 19:57:13,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:13,493] [INFO] Task started: CheckM
[2024-01-25 19:57:13,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/checkm_input GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:57:45,872] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:45,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:45,893] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:45,894] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:45,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:57:45,894] [INFO] Task started: Blastn
[2024-01-25 19:57:45,894] [INFO] Running command: blastn -query GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg43e90c99-32f7-4073-8a1f-f4923cfc6a00/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:46,655] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:46,658] [INFO] Selected 18 target genomes.
[2024-01-25 19:57:46,658] [INFO] Target genome list was writen to GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:46,677] [INFO] Task started: fastANI
[2024-01-25 19:57:46,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg277d9504-9c65-470f-8de2-5fbc4422887b/GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna.gz --refList GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:59,401] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:59,405] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:59,406] [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_900116235.1	s__Marininema halotolerans	100.0	1175	1177	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marininema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106775.1	s__Marininema mesophilum	79.2913	442	1177	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marininema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013265585.1	s__Kroppenstedtia_A pulmonis	76.688	53	1177	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_003046315.1	s__Desmospora activa	76.491	68	1177	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Desmospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:59,407] [INFO] GTDB search result was written to GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:59,407] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:59,409] [INFO] DFAST_QC result json was written to GCF_900116235.1_IMG-taxon_2675903148_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:57:59,410] [INFO] DFAST_QC completed!
[2024-01-25 19:57:59,410] [INFO] Total running time: 0h1m9s