[2024-01-24 11:51:36,951] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference
[2024-01-24 11:51:38,180] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,181] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a2b7041-d122-4c15-a4f0-9b629dfb5e84/GCF_003987575.1_ASM398757v1_genomic.fna.gz | prodigal -d GCF_003987575.1_ASM398757v1_genomic.fna/cds.fna -a GCF_003987575.1_ASM398757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:42,480] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:42,480] [INFO] Task started: HMMsearch
[2024-01-24 11:51:42,481] [INFO] Running command: hmmsearch --tblout GCF_003987575.1_ASM398757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference/reference_markers.hmm GCF_003987575.1_ASM398757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:42,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:42,722] [INFO] Found 6/6 markers.
[2024-01-24 11:51:42,746] [INFO] Query marker FASTA was written to GCF_003987575.1_ASM398757v1_genomic.fna/markers.fasta
[2024-01-24 11:51:42,746] [INFO] Task started: Blastn
[2024-01-24 11:51:42,747] [INFO] Running command: blastn -query GCF_003987575.1_ASM398757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference/reference_markers.fasta -out GCF_003987575.1_ASM398757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:43,316] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:43,320] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:43,321] [INFO] Target genome list was writen to GCF_003987575.1_ASM398757v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:43,347] [INFO] Task started: fastANI
[2024-01-24 11:51:43,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a2b7041-d122-4c15-a4f0-9b629dfb5e84/GCF_003987575.1_ASM398757v1_genomic.fna.gz --refList GCF_003987575.1_ASM398757v1_genomic.fna/target_genomes.txt --output GCF_003987575.1_ASM398757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:50,146] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:50,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:50,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:50,164] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:50,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:50,165] [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
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	100.0	870	870	95	conclusive
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	99.9942	857	870	95	conclusive
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	80.2527	433	870	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	80.174	388	870	95	below_threshold
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	78.591	224	870	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	78.4695	196	870	95	below_threshold
Vagococcus martis	strain=D7T301	GCA_002026305.1	1768210	1768210	type	True	78.4304	216	870	95	below_threshold
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	78.4146	87	870	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	78.3661	228	870	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	78.0713	104	870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:50,167] [INFO] DFAST Taxonomy check result was written to GCF_003987575.1_ASM398757v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:50,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:50,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:50,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference/checkm_data
[2024-01-24 11:51:50,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:50,204] [INFO] Task started: CheckM
[2024-01-24 11:51:50,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987575.1_ASM398757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987575.1_ASM398757v1_genomic.fna/checkm_input GCF_003987575.1_ASM398757v1_genomic.fna/checkm_result
[2024-01-24 11:52:10,715] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:10,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:10,742] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:10,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:10,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987575.1_ASM398757v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:10,744] [INFO] Task started: Blastn
[2024-01-24 11:52:10,744] [INFO] Running command: blastn -query GCF_003987575.1_ASM398757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b66e8e6-856d-498b-81b8-c32897e19e61/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987575.1_ASM398757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:11,545] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:11,550] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:11,550] [INFO] Target genome list was writen to GCF_003987575.1_ASM398757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:11,559] [INFO] Task started: fastANI
[2024-01-24 11:52:11,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a2b7041-d122-4c15-a4f0-9b629dfb5e84/GCF_003987575.1_ASM398757v1_genomic.fna.gz --refList GCF_003987575.1_ASM398757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987575.1_ASM398757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:16,553] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:16,567] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:16,567] [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_003337315.1	s__Vagococcus fluvialis	99.9942	857	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	conclusive
GCF_017316185.1	s__Vagococcus sp017316185	81.8008	454	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397115.1	s__Vagococcus carniphilus	80.2695	431	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011304195.1	s__Vagococcus hydrophili	80.1634	390	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163795.1	s__Vagococcus fluvialis_A	79.5625	364	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003462485.1	s__Vagococcus sp003462485	78.6247	214	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001870205.1	s__Vagococcus teuberi	78.6081	223	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_002026305.1	s__Vagococcus martis	78.515	213	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	N/A	N/A	N/A	N/A	1	-
GCF_004795745.1	s__Vagococcus silagei	78.4884	195	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950315.1	s__Vagococcus bubulae	78.4041	229	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,568] [INFO] GTDB search result was written to GCF_003987575.1_ASM398757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:16,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:16,572] [INFO] DFAST_QC result json was written to GCF_003987575.1_ASM398757v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:16,572] [INFO] DFAST_QC completed!
[2024-01-24 11:52:16,572] [INFO] Total running time: 0h0m40s