[2024-01-24 12:42:09,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference
[2024-01-24 12:42:10,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,949] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d49e1e9-38f7-4ab5-977f-990d2cabfa94/GCF_001545095.1_ASM154509v1_genomic.fna.gz | prodigal -d GCF_001545095.1_ASM154509v1_genomic.fna/cds.fna -a GCF_001545095.1_ASM154509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:16,799] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:16,799] [INFO] Task started: HMMsearch
[2024-01-24 12:42:16,800] [INFO] Running command: hmmsearch --tblout GCF_001545095.1_ASM154509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference/reference_markers.hmm GCF_001545095.1_ASM154509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:17,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:17,050] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4d49e1e9-38f7-4ab5-977f-990d2cabfa94/GCF_001545095.1_ASM154509v1_genomic.fna.gz]
[2024-01-24 12:42:17,076] [INFO] Query marker FASTA was written to GCF_001545095.1_ASM154509v1_genomic.fna/markers.fasta
[2024-01-24 12:42:17,077] [INFO] Task started: Blastn
[2024-01-24 12:42:17,077] [INFO] Running command: blastn -query GCF_001545095.1_ASM154509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference/reference_markers.fasta -out GCF_001545095.1_ASM154509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:17,666] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:17,669] [INFO] Selected 26 target genomes.
[2024-01-24 12:42:17,669] [INFO] Target genome list was writen to GCF_001545095.1_ASM154509v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:17,697] [INFO] Task started: fastANI
[2024-01-24 12:42:17,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d49e1e9-38f7-4ab5-977f-990d2cabfa94/GCF_001545095.1_ASM154509v1_genomic.fna.gz --refList GCF_001545095.1_ASM154509v1_genomic.fna/target_genomes.txt --output GCF_001545095.1_ASM154509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:26,077] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:26,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:26,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:26,083] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:26,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:26,083] [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
Erysipelothrix larvae	strain=LV19	GCA_001545095.1	1514105	1514105	type	True	100.0	833	836	95	conclusive
Erysipelothrix inopinata	strain=DSM 15511	GCA_014396165.1	225084	225084	type	True	78.9195	56	836	95	below_threshold
Erysipelothrix piscisicarius	strain=15TAL0474	GCA_003931795.1	2485784	2485784	type	True	78.1702	50	836	95	below_threshold
Erysipelothrix tonsillarum	strain=DSM 14972	GCA_000373785.1	38402	38402	type	True	77.4177	59	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:26,085] [INFO] DFAST Taxonomy check result was written to GCF_001545095.1_ASM154509v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:26,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:26,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:26,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference/checkm_data
[2024-01-24 12:42:26,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:26,112] [INFO] Task started: CheckM
[2024-01-24 12:42:26,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001545095.1_ASM154509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001545095.1_ASM154509v1_genomic.fna/checkm_input GCF_001545095.1_ASM154509v1_genomic.fna/checkm_result
[2024-01-24 12:42:50,817] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:50,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:50,840] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:50,840] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:50,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001545095.1_ASM154509v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:50,841] [INFO] Task started: Blastn
[2024-01-24 12:42:50,841] [INFO] Running command: blastn -query GCF_001545095.1_ASM154509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3feb634-259a-4fa6-840a-51f0addd7263/dqc_reference/reference_markers_gtdb.fasta -out GCF_001545095.1_ASM154509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:51,681] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:51,685] [INFO] Selected 24 target genomes.
[2024-01-24 12:42:51,685] [INFO] Target genome list was writen to GCF_001545095.1_ASM154509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:51,702] [INFO] Task started: fastANI
[2024-01-24 12:42:51,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d49e1e9-38f7-4ab5-977f-990d2cabfa94/GCF_001545095.1_ASM154509v1_genomic.fna.gz --refList GCF_001545095.1_ASM154509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001545095.1_ASM154509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:00,410] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:00,419] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:00,419] [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_001545095.1	s__Erysipelothrix larvae	100.0	833	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011400295.1	s__Erysipelothrix sp011400295	78.821	65	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396165.1	s__Erysipelothrix inopinata	78.5801	55	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931795.1	s__Erysipelothrix piscisicarius	78.3527	51	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	98.72	98.37	0.91	0.89	4	-
GCF_000373785.1	s__Erysipelothrix tonsillarum	77.4208	58	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:00,421] [INFO] GTDB search result was written to GCF_001545095.1_ASM154509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:00,421] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:00,424] [INFO] DFAST_QC result json was written to GCF_001545095.1_ASM154509v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:00,424] [INFO] DFAST_QC completed!
[2024-01-24 12:43:00,424] [INFO] Total running time: 0h0m51s