[2024-01-24 15:18:51,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,031] [INFO] DQC Reference Directory: /var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference
[2024-01-24 15:18:52,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,279] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,279] [INFO] Running command: gunzip -c /var/lib/cwl/stg527d9703-0e07-4236-b94d-efee233be08c/GCF_003970575.1_ASM397057v1_genomic.fna.gz | prodigal -d GCF_003970575.1_ASM397057v1_genomic.fna/cds.fna -a GCF_003970575.1_ASM397057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:56,438] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:56,438] [INFO] Task started: HMMsearch
[2024-01-24 15:18:56,438] [INFO] Running command: hmmsearch --tblout GCF_003970575.1_ASM397057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference/reference_markers.hmm GCF_003970575.1_ASM397057v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:56,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:56,704] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg527d9703-0e07-4236-b94d-efee233be08c/GCF_003970575.1_ASM397057v1_genomic.fna.gz]
[2024-01-24 15:18:56,732] [INFO] Query marker FASTA was written to GCF_003970575.1_ASM397057v1_genomic.fna/markers.fasta
[2024-01-24 15:18:56,733] [INFO] Task started: Blastn
[2024-01-24 15:18:56,733] [INFO] Running command: blastn -query GCF_003970575.1_ASM397057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference/reference_markers.fasta -out GCF_003970575.1_ASM397057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:57,390] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:57,393] [INFO] Selected 10 target genomes.
[2024-01-24 15:18:57,394] [INFO] Target genome list was writen to GCF_003970575.1_ASM397057v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:57,398] [INFO] Task started: fastANI
[2024-01-24 15:18:57,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg527d9703-0e07-4236-b94d-efee233be08c/GCF_003970575.1_ASM397057v1_genomic.fna.gz --refList GCF_003970575.1_ASM397057v1_genomic.fna/target_genomes.txt --output GCF_003970575.1_ASM397057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:04,944] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:04,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:04,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:04,952] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:04,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:04,952] [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 fleurettii	strain=DSM 13212	GCA_003970575.1	150056	150056	type	True	100.0	756	769	95	conclusive
Mammaliicoccus fleurettii	strain=NCTC13829	GCA_900458505.1	150056	150056	type	True	99.967	766	769	95	conclusive
Mammaliicoccus vitulinus	strain=FDAARGOS_1207	GCA_016889245.1	71237	71237	suspected-type	True	87.5993	665	769	95	below_threshold
Mammaliicoccus vitulinus	strain=DSM 15615	GCA_002902265.1	71237	71237	type	True	87.569	612	769	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	84.2256	623	769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:04,954] [INFO] DFAST Taxonomy check result was written to GCF_003970575.1_ASM397057v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:04,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:04,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:04,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference/checkm_data
[2024-01-24 15:19:04,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:04,991] [INFO] Task started: CheckM
[2024-01-24 15:19:04,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970575.1_ASM397057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970575.1_ASM397057v1_genomic.fna/checkm_input GCF_003970575.1_ASM397057v1_genomic.fna/checkm_result
[2024-01-24 15:19:25,571] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:25,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:25,596] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:25,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:25,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970575.1_ASM397057v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:25,597] [INFO] Task started: Blastn
[2024-01-24 15:19:25,597] [INFO] Running command: blastn -query GCF_003970575.1_ASM397057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd057f84b-93df-46ee-a5d8-2c54b5f46882/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970575.1_ASM397057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:26,336] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:26,340] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:26,340] [INFO] Target genome list was writen to GCF_003970575.1_ASM397057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:26,345] [INFO] Task started: fastANI
[2024-01-24 15:19:26,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg527d9703-0e07-4236-b94d-efee233be08c/GCF_003970575.1_ASM397057v1_genomic.fna.gz --refList GCF_003970575.1_ASM397057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970575.1_ASM397057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:30,482] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:30,492] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:30,492] [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_003970575.1	s__Mammaliicoccus fleurettii	100.0	756	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.35	98.97	0.91	0.88	9	conclusive
GCF_002902265.1	s__Mammaliicoccus vitulinus	87.5756	612	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	98.82	98.52	0.92	0.85	19	-
GCF_002901825.1	s__Mammaliicoccus sciuri	84.1942	621	769	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	81.7215	550	769	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	81.4329	483	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	100.00	100.00	1.00	0.99	3	-
GCF_002901845.1	s__Staphylococcus hominis	77.652	160	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:30,494] [INFO] GTDB search result was written to GCF_003970575.1_ASM397057v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:30,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:30,497] [INFO] DFAST_QC result json was written to GCF_003970575.1_ASM397057v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:30,497] [INFO] DFAST_QC completed!
[2024-01-24 15:19:30,498] [INFO] Total running time: 0h0m39s