[2024-01-24 13:26:26,325] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference
[2024-01-24 13:26:27,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,542] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,542] [INFO] Running command: gunzip -c /var/lib/cwl/stgacb6da02-f307-4194-ad56-10dff0eab7fa/GCF_025519785.1_ASM2551978v1_genomic.fna.gz | prodigal -d GCF_025519785.1_ASM2551978v1_genomic.fna/cds.fna -a GCF_025519785.1_ASM2551978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:31,717] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:31,718] [INFO] Task started: HMMsearch
[2024-01-24 13:26:31,718] [INFO] Running command: hmmsearch --tblout GCF_025519785.1_ASM2551978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference/reference_markers.hmm GCF_025519785.1_ASM2551978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:31,961] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:31,963] [INFO] Found 6/6 markers.
[2024-01-24 13:26:31,987] [INFO] Query marker FASTA was written to GCF_025519785.1_ASM2551978v1_genomic.fna/markers.fasta
[2024-01-24 13:26:31,987] [INFO] Task started: Blastn
[2024-01-24 13:26:31,987] [INFO] Running command: blastn -query GCF_025519785.1_ASM2551978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference/reference_markers.fasta -out GCF_025519785.1_ASM2551978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:32,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:32,580] [INFO] Selected 31 target genomes.
[2024-01-24 13:26:32,581] [INFO] Target genome list was writen to GCF_025519785.1_ASM2551978v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:32,778] [INFO] Task started: fastANI
[2024-01-24 13:26:32,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb6da02-f307-4194-ad56-10dff0eab7fa/GCF_025519785.1_ASM2551978v1_genomic.fna.gz --refList GCF_025519785.1_ASM2551978v1_genomic.fna/target_genomes.txt --output GCF_025519785.1_ASM2551978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:45,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:45,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:45,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:45,219] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:45,219] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:45,219] [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 pettenkoferi	strain=FDAARGOS_1071	GCA_016127935.1	170573	170573	type	True	79.1999	275	769	95	below_threshold
Staphylococcus pettenkoferi	strain=CCUG 51270	GCA_002902685.1	170573	170573	type	True	79.0996	267	769	95	below_threshold
Staphylococcus argensis	strain=DSM 29875	GCA_002902305.1	1607738	1607738	type	True	78.9575	282	769	95	below_threshold
Staphylococcus lloydii	strain=23_2_7_LY	GCA_015775975.1	2781774	2781774	type	True	77.9393	167	769	95	below_threshold
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_006094355.1	29385	29385	type	True	77.9344	171	769	95	below_threshold
Staphylococcus hominis	strain=NCTC 11320	GCA_900458635.1	1290	1290	type	True	77.9197	153	769	95	below_threshold
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_000010125.1	29385	29385	type	True	77.8905	174	769	95	below_threshold
Staphylococcus kloosii	strain=ATCC 43959	GCA_003019255.1	29384	29384	type	True	77.887	184	769	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	77.8803	173	769	95	below_threshold
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	77.8572	163	769	95	below_threshold
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_001997165.1	29385	29385	type	True	77.8452	169	769	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC 7292	GCA_002902025.2	29385	29385	type	True	77.8146	168	769	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	77.8019	155	769	95	below_threshold
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	77.8007	157	769	95	below_threshold
Staphylococcus pseudoxylosus	strain=S04009	GCA_003697915.1	2282419	2282419	type	True	77.7255	161	769	95	below_threshold
Staphylococcus hominis subsp. hominis	strain=NCTC 11320	GCA_002901845.1	145391	1290	type	True	77.7151	146	769	95	below_threshold
Staphylococcus xylosus	strain=NCTC 11043	GCA_002901985.1	1288	1288	type	True	77.6567	153	769	95	below_threshold
Staphylococcus simiae	strain=NCTC13838	GCA_900187055.1	308354	308354	type	True	77.6463	153	769	95	below_threshold
Staphylococcus xylosus	strain=CCM 2738	GCA_002732165.1	1288	1288	type	True	77.6454	160	769	95	below_threshold
Staphylococcus haemolyticus	strain=ATCC 29970	GCA_006094395.1	1283	1283	type	True	77.6425	160	769	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	77.6206	155	769	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC11042	GCA_900458595.1	1283	1283	type	True	77.5777	158	769	95	below_threshold
Staphylococcus debuckii	strain=SDB 2975	GCA_003718735.1	2044912	2044912	type	True	77.563	122	769	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	77.5389	165	769	95	below_threshold
Staphylococcus piscifermentans	strain=NCTC13836	GCA_900186985.1	70258	70258	type	True	77.4207	122	769	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	77.4021	155	769	95	below_threshold
Staphylococcus piscifermentans	strain=DSM 7373	GCA_003970555.1	70258	70258	type	True	77.3679	123	769	95	below_threshold
Staphylococcus simiae	strain=CCM 7213	GCA_000235645.2	308354	308354	type	True	77.3613	137	769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:45,221] [INFO] DFAST Taxonomy check result was written to GCF_025519785.1_ASM2551978v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:45,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:45,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:45,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference/checkm_data
[2024-01-24 13:26:45,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:45,259] [INFO] Task started: CheckM
[2024-01-24 13:26:45,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025519785.1_ASM2551978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025519785.1_ASM2551978v1_genomic.fna/checkm_input GCF_025519785.1_ASM2551978v1_genomic.fna/checkm_result
[2024-01-24 13:27:05,689] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:05,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:05,713] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:05,713] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:05,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025519785.1_ASM2551978v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:05,714] [INFO] Task started: Blastn
[2024-01-24 13:27:05,714] [INFO] Running command: blastn -query GCF_025519785.1_ASM2551978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2043b12f-e005-4be0-b09a-ad613a4aa20c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025519785.1_ASM2551978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:06,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:06,455] [INFO] Selected 28 target genomes.
[2024-01-24 13:27:06,455] [INFO] Target genome list was writen to GCF_025519785.1_ASM2551978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:06,763] [INFO] Task started: fastANI
[2024-01-24 13:27:06,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb6da02-f307-4194-ad56-10dff0eab7fa/GCF_025519785.1_ASM2551978v1_genomic.fna.gz --refList GCF_025519785.1_ASM2551978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025519785.1_ASM2551978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:18,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:18,970] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:27:18,971] [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_002902685.1	s__Staphylococcus pettenkoferi	79.0996	267	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.48	96.01	0.95	0.89	21	-
GCF_002902305.1	s__Staphylococcus argensis	78.9414	283	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.94	1.00	1.00	8	-
GCF_015775975.1	s__Staphylococcus lloydii	77.9676	164	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.39	98.19	0.98	0.95	4	-
GCF_014635045.1	s__Staphylococcus nepalensis	77.8787	159	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.49	99.27	0.96	0.93	23	-
GCF_003019255.1	s__Staphylococcus kloosii	77.8722	183	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_000010125.1	s__Staphylococcus saprophyticus	77.8673	173	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_016774515.1	s__Staphylococcus xylosus_A	77.8344	169	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_002902235.1	s__Staphylococcus ureilyticus	77.8007	157	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_002902405.1	s__Staphylococcus schweitzeri	77.7501	146	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	77.7255	161	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_002901845.1	s__Staphylococcus hominis	77.711	147	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
GCF_000875895.1	s__Staphylococcus gallinarum	77.678	180	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_013391405.1	s__Staphylococcus sp013391405	77.6624	174	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003491325.1	s__Staphylococcus warneri_A	77.6558	171	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902345.1	s__Staphylococcus arlettae	77.6526	165	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.12	98.73	0.94	0.91	41	-
GCF_002732165.1	s__Staphylococcus xylosus	77.6454	160	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_002902085.1	s__Staphylococcus simiae	77.6408	145	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
GCF_017357005.1	s__Staphylococcus simiae_A	77.6309	144	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.91	0.98	0.98	6	-
GCF_001618885.1	s__Staphylococcus condimenti	77.6004	128	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.75	99.00	0.98	0.93	11	-
GCF_006094395.1	s__Staphylococcus haemolyticus	77.5961	161	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_003718735.1	s__Staphylococcus debuckii	77.5949	120	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338275.1	s__Staphylococcus xylosus_B	77.5648	164	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_900458435.1	s__Staphylococcus carnosus	77.4809	138	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
GCF_003970495.1	s__Staphylococcus pasteuri	77.464	159	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002902725.1	s__Staphylococcus caprae	77.4474	169	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCA_900186985.1	s__Staphylococcus piscifermentans	77.4207	122	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_002902525.1	s__Mammaliicoccus stepanovicii	77.294	78	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	100.00	100.00	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:18,975] [INFO] GTDB search result was written to GCF_025519785.1_ASM2551978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:18,976] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:18,982] [INFO] DFAST_QC result json was written to GCF_025519785.1_ASM2551978v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:18,982] [INFO] DFAST_QC completed!
[2024-01-24 13:27:18,982] [INFO] Total running time: 0h0m53s