[2024-01-24 12:14:09,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference
[2024-01-24 12:14:10,368] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:10,369] [INFO] Task started: Prodigal
[2024-01-24 12:14:10,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f6bbc1e-de30-4cb2-806f-42c69ee9507b/GCF_000160815.2_ASM16081v2_genomic.fna.gz | prodigal -d GCF_000160815.2_ASM16081v2_genomic.fna/cds.fna -a GCF_000160815.2_ASM16081v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:14,159] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:14,159] [INFO] Task started: HMMsearch
[2024-01-24 12:14:14,159] [INFO] Running command: hmmsearch --tblout GCF_000160815.2_ASM16081v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference/reference_markers.hmm GCF_000160815.2_ASM16081v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:14,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:14,392] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f6bbc1e-de30-4cb2-806f-42c69ee9507b/GCF_000160815.2_ASM16081v2_genomic.fna.gz]
[2024-01-24 12:14:14,414] [INFO] Query marker FASTA was written to GCF_000160815.2_ASM16081v2_genomic.fna/markers.fasta
[2024-01-24 12:14:14,414] [INFO] Task started: Blastn
[2024-01-24 12:14:14,415] [INFO] Running command: blastn -query GCF_000160815.2_ASM16081v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference/reference_markers.fasta -out GCF_000160815.2_ASM16081v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:14,985] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:14,989] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:14,989] [INFO] Target genome list was writen to GCF_000160815.2_ASM16081v2_genomic.fna/target_genomes.txt
[2024-01-24 12:14:15,050] [INFO] Task started: fastANI
[2024-01-24 12:14:15,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6bbc1e-de30-4cb2-806f-42c69ee9507b/GCF_000160815.2_ASM16081v2_genomic.fna.gz --refList GCF_000160815.2_ASM16081v2_genomic.fna/target_genomes.txt --output GCF_000160815.2_ASM16081v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:20,699] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:20,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:20,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:20,708] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:20,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:20,709] [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 rhusiopathiae	strain=ATCC 19414	GCA_000160815.2	1648	1648	type	True	100.0	580	581	95	conclusive
Erysipelothrix rhusiopathiae	strain=NCTC8163	GCA_900637845.1	1648	1648	type	True	99.9988	581	581	95	conclusive
Erysipelothrix piscisicarius	strain=15TAL0474	GCA_003931795.1	2485784	2485784	type	True	87.8148	476	581	95	below_threshold
Erysipelothrix tonsillarum	strain=DSM 14972	GCA_000373785.1	38402	38402	type	True	83.9328	405	581	95	below_threshold
Erysipelothrix inopinata	strain=DSM 15511	GCA_014396165.1	225084	225084	type	True	79.0377	133	581	95	below_threshold
Erysipelothrix anatis	strain=D17_0559-3-2-1	GCA_009828745.1	2683713	2683713	type	True	78.4931	101	581	95	below_threshold
Erysipelothrix urinaevulpis	strain=165301687	GCA_009828835.1	2683717	2683717	type	True	77.9425	74	581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:20,710] [INFO] DFAST Taxonomy check result was written to GCF_000160815.2_ASM16081v2_genomic.fna/tc_result.tsv
[2024-01-24 12:14:20,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:20,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:20,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference/checkm_data
[2024-01-24 12:14:20,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:20,732] [INFO] Task started: CheckM
[2024-01-24 12:14:20,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000160815.2_ASM16081v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000160815.2_ASM16081v2_genomic.fna/checkm_input GCF_000160815.2_ASM16081v2_genomic.fna/checkm_result
[2024-01-24 12:14:40,090] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:40,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:40,115] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:40,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:40,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000160815.2_ASM16081v2_genomic.fna/markers.fasta)
[2024-01-24 12:14:40,116] [INFO] Task started: Blastn
[2024-01-24 12:14:40,116] [INFO] Running command: blastn -query GCF_000160815.2_ASM16081v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bf8620f-a30e-4c21-b931-d3941119a963/dqc_reference/reference_markers_gtdb.fasta -out GCF_000160815.2_ASM16081v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:41,019] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:41,025] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:41,025] [INFO] Target genome list was writen to GCF_000160815.2_ASM16081v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:41,041] [INFO] Task started: fastANI
[2024-01-24 12:14:41,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6bbc1e-de30-4cb2-806f-42c69ee9507b/GCF_000160815.2_ASM16081v2_genomic.fna.gz --refList GCF_000160815.2_ASM16081v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000160815.2_ASM16081v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:45,583] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:45,591] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:45,591] [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_900637845.1	s__Erysipelothrix rhusiopathiae	99.9988	580	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	98.98	96.63	0.95	0.91	13	conclusive
GCF_003931795.1	s__Erysipelothrix piscisicarius	87.7966	478	581	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	83.9441	405	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011301115.1	s__Erysipelothrix sp011301115	79.3724	110	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	98.38	96.88	0.92	0.88	5	-
GCF_011400295.1	s__Erysipelothrix sp011400295	79.2275	98	581	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	79.1593	134	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828835.1	s__Erysipelothrix sp009828835	77.8954	75	581	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 12:14:45,593] [INFO] GTDB search result was written to GCF_000160815.2_ASM16081v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:45,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:45,600] [INFO] DFAST_QC result json was written to GCF_000160815.2_ASM16081v2_genomic.fna/dqc_result.json
[2024-01-24 12:14:45,600] [INFO] DFAST_QC completed!
[2024-01-24 12:14:45,601] [INFO] Total running time: 0h0m37s