[2024-01-25 18:52:05,397] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:05,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:05,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference
[2024-01-25 18:52:06,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:06,498] [INFO] Task started: Prodigal
[2024-01-25 18:52:06,498] [INFO] Running command: gunzip -c /var/lib/cwl/stge767ffd9-7a2c-4bb1-b488-db9b23a4f736/GCF_014634985.1_ASM1463498v1_genomic.fna.gz | prodigal -d GCF_014634985.1_ASM1463498v1_genomic.fna/cds.fna -a GCF_014634985.1_ASM1463498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:10,308] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:10,308] [INFO] Task started: HMMsearch
[2024-01-25 18:52:10,308] [INFO] Running command: hmmsearch --tblout GCF_014634985.1_ASM1463498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference/reference_markers.hmm GCF_014634985.1_ASM1463498v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:10,512] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:10,513] [INFO] Found 6/6 markers.
[2024-01-25 18:52:10,534] [INFO] Query marker FASTA was written to GCF_014634985.1_ASM1463498v1_genomic.fna/markers.fasta
[2024-01-25 18:52:10,535] [INFO] Task started: Blastn
[2024-01-25 18:52:10,535] [INFO] Running command: blastn -query GCF_014634985.1_ASM1463498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference/reference_markers.fasta -out GCF_014634985.1_ASM1463498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:11,084] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:11,086] [INFO] Selected 14 target genomes.
[2024-01-25 18:52:11,087] [INFO] Target genome list was writen to GCF_014634985.1_ASM1463498v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:11,099] [INFO] Task started: fastANI
[2024-01-25 18:52:11,099] [INFO] Running command: fastANI --query /var/lib/cwl/stge767ffd9-7a2c-4bb1-b488-db9b23a4f736/GCF_014634985.1_ASM1463498v1_genomic.fna.gz --refList GCF_014634985.1_ASM1463498v1_genomic.fna/target_genomes.txt --output GCF_014634985.1_ASM1463498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:17,373] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:17,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:17,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:17,381] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:52:17,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:17,381] [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
Macrococcus hajekii	strain=CCM 4809	GCA_014634985.1	198482	198482	type	True	100.0	678	679	95	conclusive
Macrococcus hajekii	strain=CCM4809	GCA_004359505.1	198482	198482	type	True	99.9977	675	679	95	conclusive
Macrococcus carouselicus	strain=ATCC 51828	GCA_004359515.1	69969	69969	type	True	80.3412	375	679	95	below_threshold
Macrococcus brunensis	strain=CCM4811	GCA_004359615.1	198483	198483	type	True	80.2932	366	679	95	below_threshold
Macrococcus bovicus	strain=ATCC 51825	GCA_004359575.1	69968	69968	type	True	79.9132	343	679	95	below_threshold
Macrococcus equipercicus	strain=ATCC 51831	GCA_004359525.2	69967	69967	type	True	79.3259	204	679	95	below_threshold
Mammaliicoccus fleurettii	strain=NCTC13829	GCA_900458505.1	150056	150056	type	True	78.5813	65	679	95	below_threshold
Macrococcus lamae	strain=CCM4815	GCA_004359545.1	198484	198484	type	True	78.5613	199	679	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC12103	GCA_900474615.1	1296	1296	type	True	77.8778	77	679	95	below_threshold
Staphylococcus carnosus	strain=FDAARGOS_883	GCA_016028275.1	1281	1281	type	True	77.6147	53	679	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	77.5827	76	679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:17,383] [INFO] DFAST Taxonomy check result was written to GCF_014634985.1_ASM1463498v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:17,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:17,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:17,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference/checkm_data
[2024-01-25 18:52:17,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:17,406] [INFO] Task started: CheckM
[2024-01-25 18:52:17,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014634985.1_ASM1463498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014634985.1_ASM1463498v1_genomic.fna/checkm_input GCF_014634985.1_ASM1463498v1_genomic.fna/checkm_result
[2024-01-25 18:52:35,695] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:35,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:35,722] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:35,722] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:35,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014634985.1_ASM1463498v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:35,722] [INFO] Task started: Blastn
[2024-01-25 18:52:35,722] [INFO] Running command: blastn -query GCF_014634985.1_ASM1463498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cf852c6-fcb1-4fb9-bf69-3092d5ef4a07/dqc_reference/reference_markers_gtdb.fasta -out GCF_014634985.1_ASM1463498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:36,547] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:36,551] [INFO] Selected 16 target genomes.
[2024-01-25 18:52:36,552] [INFO] Target genome list was writen to GCF_014634985.1_ASM1463498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:36,563] [INFO] Task started: fastANI
[2024-01-25 18:52:36,564] [INFO] Running command: fastANI --query /var/lib/cwl/stge767ffd9-7a2c-4bb1-b488-db9b23a4f736/GCF_014634985.1_ASM1463498v1_genomic.fna.gz --refList GCF_014634985.1_ASM1463498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014634985.1_ASM1463498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:43,446] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:43,455] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:43,455] [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_004359505.1	s__Macrococcus hajekii	99.9977	675	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_004359515.1	s__Macrococcus carouselicus	80.3398	376	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359615.1	s__Macrococcus brunensis	80.2932	366	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359575.1	s__Macrococcus bovicus	79.9132	343	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359525.2	s__Macrococcus equipercicus	79.3259	204	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117835.1	s__Macrococcus_B sp004117835	78.8104	120	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970575.1	s__Mammaliicoccus fleurettii	78.585	61	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.35	98.97	0.91	0.88	9	-
GCF_004359545.1	s__Macrococcus lamae	78.5613	199	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438305.1	s__Macrococcus sp002438305	77.9373	136	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	98.53	98.53	0.76	0.76	2	-
GCF_002901825.1	s__Mammaliicoccus sciuri	77.8474	75	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_006094395.1	s__Staphylococcus haemolyticus	77.8073	52	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_002902285.1	s__Staphylococcus simulans	77.3647	65	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_002902305.1	s__Staphylococcus argensis	77.1768	50	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.94	1.00	1.00	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:43,456] [INFO] GTDB search result was written to GCF_014634985.1_ASM1463498v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:43,457] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:43,460] [INFO] DFAST_QC result json was written to GCF_014634985.1_ASM1463498v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:43,460] [INFO] DFAST_QC completed!
[2024-01-25 18:52:43,460] [INFO] Total running time: 0h0m38s