[2024-01-25 18:06:35,770] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,772] [INFO] DQC Reference Directory: /var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference
[2024-01-25 18:06:36,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,888] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,888] [INFO] Running command: gunzip -c /var/lib/cwl/stgbef1d385-13c4-4c1d-aa20-2eda69b5ab22/GCF_002902455.1_ASM290245v1_genomic.fna.gz | prodigal -d GCF_002902455.1_ASM290245v1_genomic.fna/cds.fna -a GCF_002902455.1_ASM290245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:40,670] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:40,671] [INFO] Task started: HMMsearch
[2024-01-25 18:06:40,671] [INFO] Running command: hmmsearch --tblout GCF_002902455.1_ASM290245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference/reference_markers.hmm GCF_002902455.1_ASM290245v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:40,890] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:40,891] [INFO] Found 6/6 markers.
[2024-01-25 18:06:40,912] [INFO] Query marker FASTA was written to GCF_002902455.1_ASM290245v1_genomic.fna/markers.fasta
[2024-01-25 18:06:40,912] [INFO] Task started: Blastn
[2024-01-25 18:06:40,912] [INFO] Running command: blastn -query GCF_002902455.1_ASM290245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference/reference_markers.fasta -out GCF_002902455.1_ASM290245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:41,478] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:41,481] [INFO] Selected 16 target genomes.
[2024-01-25 18:06:41,481] [INFO] Target genome list was writen to GCF_002902455.1_ASM290245v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:41,488] [INFO] Task started: fastANI
[2024-01-25 18:06:41,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgbef1d385-13c4-4c1d-aa20-2eda69b5ab22/GCF_002902455.1_ASM290245v1_genomic.fna.gz --refList GCF_002902455.1_ASM290245v1_genomic.fna/target_genomes.txt --output GCF_002902455.1_ASM290245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:48,249] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:48,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:48,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:48,260] [INFO] Found 16 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:06:48,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:48,260] [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
Staphylococcus auricularis	strain=NCTC 12101	GCA_002902455.1	29379	29379	type	True	100.0	687	688	95	conclusive
Staphylococcus auricularis	strain=FDAARGOS_882	GCA_016028295.1	29379	29379	type	True	99.9976	688	688	95	conclusive
Staphylococcus auricularis	strain=NCTC12101	GCA_900478415.1	29379	29379	type	True	99.9958	687	688	95	conclusive
Staphylococcus auricularis	strain=DSM 20609	GCA_001500315.1	29379	29379	type	True	99.9815	680	688	95	conclusive
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	78.4159	208	688	95	below_threshold
Staphylococcus croceilyticus	strain=CCUG 62728	GCA_002902575.1	319942	319942	type	True	78.385	207	688	95	below_threshold
Staphylococcus pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	78.3617	187	688	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	78.3393	174	688	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	78.313	179	688	95	below_threshold
Staphylococcus warneri	strain=NCTC 11044	GCA_002901765.1	1292	1292	type	True	78.2965	194	688	95	below_threshold
Staphylococcus pettenkoferi	strain=FDAARGOS_1071	GCA_016127935.1	170573	170573	type	True	78.274	198	688	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	78.2134	183	688	95	below_threshold
Staphylococcus pettenkoferi	strain=CCUG 51270	GCA_002902685.1	170573	170573	type	True	78.1924	198	688	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.1001	177	688	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.095	179	688	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	77.7559	123	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:48,262] [INFO] DFAST Taxonomy check result was written to GCF_002902455.1_ASM290245v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:48,263] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:48,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:48,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference/checkm_data
[2024-01-25 18:06:48,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:48,291] [INFO] Task started: CheckM
[2024-01-25 18:06:48,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902455.1_ASM290245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902455.1_ASM290245v1_genomic.fna/checkm_input GCF_002902455.1_ASM290245v1_genomic.fna/checkm_result
[2024-01-25 18:07:06,454] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:06,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:06,521] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:06,521] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:06,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902455.1_ASM290245v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:06,521] [INFO] Task started: Blastn
[2024-01-25 18:07:06,522] [INFO] Running command: blastn -query GCF_002902455.1_ASM290245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacea3686-de38-4f1b-a4c0-46dff5a74526/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902455.1_ASM290245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:07,375] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:07,378] [INFO] Selected 28 target genomes.
[2024-01-25 18:07:07,379] [INFO] Target genome list was writen to GCF_002902455.1_ASM290245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:07,443] [INFO] Task started: fastANI
[2024-01-25 18:07:07,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgbef1d385-13c4-4c1d-aa20-2eda69b5ab22/GCF_002902455.1_ASM290245v1_genomic.fna.gz --refList GCF_002902455.1_ASM290245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902455.1_ASM290245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:20,720] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:20,737] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:20,737] [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_001500315.1	s__Staphylococcus auricularis	99.9815	680	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.97	95.76	0.97	0.93	10	conclusive
GCF_900097965.1	s__Staphylococcus caeli	78.5259	195	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001224225.1	s__Staphylococcus borealis	78.5102	183	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002902235.1	s__Staphylococcus ureilyticus	78.4823	186	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_002902725.1	s__Staphylococcus caprae	78.4138	178	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCA_002902575.1	s__Staphylococcus croceilyticus	78.385	207	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_000010125.1	s__Staphylococcus saprophyticus	78.3784	212	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_006094395.1	s__Staphylococcus haemolyticus	78.3694	181	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.3588	187	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_900636385.1	s__Staphylococcus warneri	78.3145	196	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_003035445.1	s__Staphylococcus devriesei_A	78.3036	200	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_002902565.1	s__Staphylococcus petrasii	78.2731	212	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_002902285.1	s__Staphylococcus simulans	78.2599	192	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_003491325.1	s__Staphylococcus warneri_A	78.2482	190	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902305.1	s__Staphylococcus argensis	78.2267	211	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.94	1.00	1.00	8	-
GCF_001027105.1	s__Staphylococcus aureus	78.2189	176	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.78	97.08	0.95	0.88	13059	-
GCF_003718735.1	s__Staphylococcus debuckii	78.2098	159	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900458435.1	s__Staphylococcus carnosus	78.1954	168	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
GCF_002902685.1	s__Staphylococcus pettenkoferi	78.1694	200	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.48	96.01	0.95	0.89	21	-
GCF_000875895.1	s__Staphylococcus gallinarum	78.1448	205	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_001431205.1	s__Staphylococcus sp001431205	78.1377	192	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902365.1	s__Staphylococcus cohnii	78.0929	205	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_013391405.1	s__Staphylococcus sp013391405	77.9681	219	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934465.1	s__Staphylococcus microti	77.9417	129	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_002614725.1	s__Staphylococcus edaphicus	77.936	196	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747895.1	s__Staphylococcus equorum_A	77.7533	217	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_003012915.1	s__Staphylococcus felis	77.6641	100	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCF_002902085.1	s__Staphylococcus simiae	77.6332	171	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:20,739] [INFO] GTDB search result was written to GCF_002902455.1_ASM290245v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:20,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:20,743] [INFO] DFAST_QC result json was written to GCF_002902455.1_ASM290245v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:20,743] [INFO] DFAST_QC completed!
[2024-01-25 18:07:20,743] [INFO] Total running time: 0h0m45s