[2024-01-24 13:40:30,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference
[2024-01-24 13:40:31,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,587] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a56843e-43c6-4ca2-b86d-632bf5f48a2d/GCF_900458355.1_50305_E01_genomic.fna.gz | prodigal -d GCF_900458355.1_50305_E01_genomic.fna/cds.fna -a GCF_900458355.1_50305_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:35,833] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:35,834] [INFO] Task started: HMMsearch
[2024-01-24 13:40:35,834] [INFO] Running command: hmmsearch --tblout GCF_900458355.1_50305_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference/reference_markers.hmm GCF_900458355.1_50305_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:36,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:36,148] [INFO] Found 6/6 markers.
[2024-01-24 13:40:36,170] [INFO] Query marker FASTA was written to GCF_900458355.1_50305_E01_genomic.fna/markers.fasta
[2024-01-24 13:40:36,170] [INFO] Task started: Blastn
[2024-01-24 13:40:36,171] [INFO] Running command: blastn -query GCF_900458355.1_50305_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference/reference_markers.fasta -out GCF_900458355.1_50305_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:36,775] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:36,779] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:36,780] [INFO] Target genome list was writen to GCF_900458355.1_50305_E01_genomic.fna/target_genomes.txt
[2024-01-24 13:40:36,805] [INFO] Task started: fastANI
[2024-01-24 13:40:36,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a56843e-43c6-4ca2-b86d-632bf5f48a2d/GCF_900458355.1_50305_E01_genomic.fna.gz --refList GCF_900458355.1_50305_E01_genomic.fna/target_genomes.txt --output GCF_900458355.1_50305_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:45,542] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:45,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:45,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:45,553] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:45,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:45,553] [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 devriesei	strain=NCTC13828	GCA_900458355.1	586733	586733	type	True	100.0	798	799	95	conclusive
Staphylococcus devriesei	strain=CCUG 58238	GCA_002902625.1	586733	586733	type	True	99.8932	729	799	95	conclusive
Staphylococcus caledonicus	strain=H8/1	GCA_016238465.1	2741333	2741333	type	True	92.9036	720	799	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	82.5779	576	799	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	82.3104	548	799	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_004785665.1	1611836	1611836	type	True	82.2914	549	799	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_014635505.1	1611836	1611836	type	True	82.2324	547	799	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	82.204	594	799	95	below_threshold
Staphylococcus croceilyticus	strain=CCUG 62728	GCA_002902575.1	319942	319942	type	True	82.1448	538	799	95	below_threshold
Staphylococcus hominis subsp. hominis	strain=NCTC 11320	GCA_002901845.1	145391	1290	type	True	80.6491	450	799	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.5197	305	799	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.2016	282	799	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	78.7006	248	799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:45,555] [INFO] DFAST Taxonomy check result was written to GCF_900458355.1_50305_E01_genomic.fna/tc_result.tsv
[2024-01-24 13:40:45,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:45,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:45,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference/checkm_data
[2024-01-24 13:40:45,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:45,581] [INFO] Task started: CheckM
[2024-01-24 13:40:45,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458355.1_50305_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458355.1_50305_E01_genomic.fna/checkm_input GCF_900458355.1_50305_E01_genomic.fna/checkm_result
[2024-01-24 13:41:06,726] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:06,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,748] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:06,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:06,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458355.1_50305_E01_genomic.fna/markers.fasta)
[2024-01-24 13:41:06,749] [INFO] Task started: Blastn
[2024-01-24 13:41:06,749] [INFO] Running command: blastn -query GCF_900458355.1_50305_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgff35e6d7-ba8e-4abc-bd07-fa4fa2de30df/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458355.1_50305_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:07,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:07,629] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:07,629] [INFO] Target genome list was writen to GCF_900458355.1_50305_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:07,641] [INFO] Task started: fastANI
[2024-01-24 13:41:07,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a56843e-43c6-4ca2-b86d-632bf5f48a2d/GCF_900458355.1_50305_E01_genomic.fna.gz --refList GCF_900458355.1_50305_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900458355.1_50305_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:14,119] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,128] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:14,128] [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_002902625.1	s__Staphylococcus devriesei	99.8932	729	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	conclusive
GCF_003035445.1	s__Staphylococcus devriesei_A	93.1649	684	799	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	82.3011	549	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_004785665.1	s__Staphylococcus pragensis	82.277	550	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCA_002902575.1	s__Staphylococcus croceilyticus	82.159	537	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_006094395.1	s__Staphylococcus haemolyticus	81.7101	561	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_001224225.1	s__Staphylococcus borealis	81.5646	557	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002901845.1	s__Staphylococcus hominis	80.6491	450	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
GCF_900636385.1	s__Staphylococcus warneri	79.8615	375	799	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,130] [INFO] GTDB search result was written to GCF_900458355.1_50305_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:14,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:14,133] [INFO] DFAST_QC result json was written to GCF_900458355.1_50305_E01_genomic.fna/dqc_result.json
[2024-01-24 13:41:14,134] [INFO] DFAST_QC completed!
[2024-01-24 13:41:14,134] [INFO] Total running time: 0h0m44s