[2024-01-24 13:48:59,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference
[2024-01-24 13:49:01,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,130] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,130] [INFO] Running command: gunzip -c /var/lib/cwl/stgadf73fe9-b533-4e5c-b489-39075459b2ac/GCF_002902265.1_ASM290226v1_genomic.fna.gz | prodigal -d GCF_002902265.1_ASM290226v1_genomic.fna/cds.fna -a GCF_002902265.1_ASM290226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:05,291] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:05,291] [INFO] Task started: HMMsearch
[2024-01-24 13:49:05,291] [INFO] Running command: hmmsearch --tblout GCF_002902265.1_ASM290226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference/reference_markers.hmm GCF_002902265.1_ASM290226v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:05,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:05,532] [INFO] Found 6/6 markers.
[2024-01-24 13:49:05,561] [INFO] Query marker FASTA was written to GCF_002902265.1_ASM290226v1_genomic.fna/markers.fasta
[2024-01-24 13:49:05,562] [INFO] Task started: Blastn
[2024-01-24 13:49:05,562] [INFO] Running command: blastn -query GCF_002902265.1_ASM290226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference/reference_markers.fasta -out GCF_002902265.1_ASM290226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:06,152] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:06,156] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:06,156] [INFO] Target genome list was writen to GCF_002902265.1_ASM290226v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:06,162] [INFO] Task started: fastANI
[2024-01-24 13:49:06,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf73fe9-b533-4e5c-b489-39075459b2ac/GCF_002902265.1_ASM290226v1_genomic.fna.gz --refList GCF_002902265.1_ASM290226v1_genomic.fna/target_genomes.txt --output GCF_002902265.1_ASM290226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:15,014] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:15,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:15,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:15,022] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:15,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:15,022] [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
Mammaliicoccus vitulinus	strain=DSM 15615	GCA_002902265.1	71237	71237	type	True	100.0	759	764	95	conclusive
Mammaliicoccus vitulinus	strain=FDAARGOS_1207	GCA_016889245.1	71237	71237	suspected-type	True	99.9956	763	764	95	conclusive
Mammaliicoccus fleurettii	strain=DSM 13212	GCA_003970575.1	150056	150056	type	True	87.6685	612	764	95	below_threshold
Mammaliicoccus fleurettii	strain=NCTC13829	GCA_900458505.1	150056	150056	type	True	87.5631	660	764	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC12103	GCA_900474615.1	1296	1296	type	True	84.2799	634	764	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	84.2551	637	764	95	below_threshold
Mammaliicoccus stepanovicii	strain=CCM 7717	GCA_014635785.1	643214	643214	type	True	81.381	467	764	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:15,025] [INFO] DFAST Taxonomy check result was written to GCF_002902265.1_ASM290226v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:15,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:15,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:15,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference/checkm_data
[2024-01-24 13:49:15,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:15,057] [INFO] Task started: CheckM
[2024-01-24 13:49:15,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902265.1_ASM290226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902265.1_ASM290226v1_genomic.fna/checkm_input GCF_002902265.1_ASM290226v1_genomic.fna/checkm_result
[2024-01-24 13:49:35,463] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:35,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,481] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:35,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:35,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902265.1_ASM290226v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:35,482] [INFO] Task started: Blastn
[2024-01-24 13:49:35,483] [INFO] Running command: blastn -query GCF_002902265.1_ASM290226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde71dff-7d33-43a4-9dc0-4e24f1831c40/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902265.1_ASM290226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:36,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:36,279] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:36,279] [INFO] Target genome list was writen to GCF_002902265.1_ASM290226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:36,285] [INFO] Task started: fastANI
[2024-01-24 13:49:36,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf73fe9-b533-4e5c-b489-39075459b2ac/GCF_002902265.1_ASM290226v1_genomic.fna.gz --refList GCF_002902265.1_ASM290226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902265.1_ASM290226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:41,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:41,353] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:41,354] [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_002902265.1	s__Mammaliicoccus vitulinus	100.0	759	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	98.82	98.52	0.92	0.85	19	conclusive
GCF_003970575.1	s__Mammaliicoccus fleurettii	87.6793	611	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.35	98.97	0.91	0.88	9	-
GCF_002901825.1	s__Mammaliicoccus sciuri	84.1897	639	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_002902755.1	s__Mammaliicoccus lentus	81.9815	524	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.03	97.66	0.94	0.90	21	-
GCF_002902525.1	s__Mammaliicoccus stepanovicii	81.3458	464	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	100.00	100.00	1.00	0.99	3	-
GCF_002742385.2	s__Macrococcus_B goetzii	77.7052	111	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	96.60	96.57	0.86	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,355] [INFO] GTDB search result was written to GCF_002902265.1_ASM290226v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:41,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:41,359] [INFO] DFAST_QC result json was written to GCF_002902265.1_ASM290226v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:41,360] [INFO] DFAST_QC completed!
[2024-01-24 13:49:41,360] [INFO] Total running time: 0h0m41s