[2024-01-24 10:48:09,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,167] [INFO] DQC Reference Directory: /var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg63eb09a8-a90a-48e8-b001-ead1da57313f/GCF_003815035.1_ASM381503v1_genomic.fna.gz | prodigal -d GCF_003815035.1_ASM381503v1_genomic.fna/cds.fna -a GCF_003815035.1_ASM381503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:27,611] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:27,611] [INFO] Task started: HMMsearch
[2024-01-24 10:48:27,612] [INFO] Running command: hmmsearch --tblout GCF_003815035.1_ASM381503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference/reference_markers.hmm GCF_003815035.1_ASM381503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:27,842] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:27,843] [INFO] Found 6/6 markers.
[2024-01-24 10:48:27,865] [INFO] Query marker FASTA was written to GCF_003815035.1_ASM381503v1_genomic.fna/markers.fasta
[2024-01-24 10:48:27,865] [INFO] Task started: Blastn
[2024-01-24 10:48:27,865] [INFO] Running command: blastn -query GCF_003815035.1_ASM381503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference/reference_markers.fasta -out GCF_003815035.1_ASM381503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:29,049] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:29,054] [INFO] Selected 27 target genomes.
[2024-01-24 10:48:29,054] [INFO] Target genome list was writen to GCF_003815035.1_ASM381503v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:29,902] [INFO] Task started: fastANI
[2024-01-24 10:48:29,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg63eb09a8-a90a-48e8-b001-ead1da57313f/GCF_003815035.1_ASM381503v1_genomic.fna.gz --refList GCF_003815035.1_ASM381503v1_genomic.fna/target_genomes.txt --output GCF_003815035.1_ASM381503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:40,664] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:40,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:40,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:40,680] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:40,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:40,680] [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
Abyssicoccus albus	strain=DSM 29158	GCA_003815035.1	1817405	1817405	type	True	100.0	592	593	95	conclusive
Mammaliicoccus stepanovicii	strain=CCM 7717	GCA_014635785.1	643214	643214	type	True	77.7093	57	593	95	below_threshold
Staphylococcus felis	strain=FDAARGOS_1014	GCA_016127055.1	46127	46127	type	True	77.4509	52	593	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	77.4056	50	593	95	below_threshold
Staphylococcus felis	strain=ATCC 49168	GCA_003012915.1	46127	46127	type	True	77.3671	52	593	95	below_threshold
Staphylococcus warneri	strain=NCTC11044	GCA_900636385.1	1292	1292	type	True	77.0781	59	593	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC12103	GCA_900474615.1	1296	1296	type	True	76.9918	65	593	95	below_threshold
Staphylococcus pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	76.9255	50	593	95	below_threshold
Staphylococcus warneri	strain=NCTC 11044	GCA_002901765.1	1292	1292	type	True	76.8786	56	593	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	76.6824	67	593	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC 12103	GCA_002901825.1	1296	1296	type	True	76.6228	63	593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:40,682] [INFO] DFAST Taxonomy check result was written to GCF_003815035.1_ASM381503v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:40,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:40,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:40,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference/checkm_data
[2024-01-24 10:48:40,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:40,710] [INFO] Task started: CheckM
[2024-01-24 10:48:40,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003815035.1_ASM381503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003815035.1_ASM381503v1_genomic.fna/checkm_input GCF_003815035.1_ASM381503v1_genomic.fna/checkm_result
[2024-01-24 10:49:01,002] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:01,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:01,097] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:01,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:01,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003815035.1_ASM381503v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:01,098] [INFO] Task started: Blastn
[2024-01-24 10:49:01,098] [INFO] Running command: blastn -query GCF_003815035.1_ASM381503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd508a406-d973-437e-8e3e-3ce5291e9fa0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003815035.1_ASM381503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:02,403] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:02,407] [INFO] Selected 25 target genomes.
[2024-01-24 10:49:02,407] [INFO] Target genome list was writen to GCF_003815035.1_ASM381503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:02,524] [INFO] Task started: fastANI
[2024-01-24 10:49:02,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg63eb09a8-a90a-48e8-b001-ead1da57313f/GCF_003815035.1_ASM381503v1_genomic.fna.gz --refList GCF_003815035.1_ASM381503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003815035.1_ASM381503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:15,619] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:15,628] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:15,628] [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_003815035.1	s__Abyssicoccus albus	100.0	592	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__DSM-29158;g__Abyssicoccus	95.0	98.05	98.05	0.90	0.90	2	conclusive
GCF_004117835.1	s__Macrococcus_B sp004117835	77.6677	66	593	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_003491325.1	s__Staphylococcus warneri_A	77.5914	52	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_000236925.1	s__Staphylococcus argenteus	77.5776	52	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	-
GCF_003012915.1	s__Staphylococcus felis	77.3671	52	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCF_002902525.1	s__Mammaliicoccus stepanovicii	77.2308	56	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900636385.1	s__Staphylococcus warneri	77.0781	59	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_003970495.1	s__Staphylococcus pasteuri	76.9255	50	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002901825.1	s__Mammaliicoccus sciuri	76.6228	63	593	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:15,639] [INFO] GTDB search result was written to GCF_003815035.1_ASM381503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:15,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:15,644] [INFO] DFAST_QC result json was written to GCF_003815035.1_ASM381503v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:15,644] [INFO] DFAST_QC completed!
[2024-01-24 10:49:15,644] [INFO] Total running time: 0h1m6s