[2024-01-25 19:41:35,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:35,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:35,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference
[2024-01-25 19:41:36,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:36,655] [INFO] Task started: Prodigal
[2024-01-25 19:41:36,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg03daf248-c769-4125-ab04-1124565f2f17/GCF_002902405.1_ASM290240v1_genomic.fna.gz | prodigal -d GCF_002902405.1_ASM290240v1_genomic.fna/cds.fna -a GCF_002902405.1_ASM290240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:40,946] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:40,946] [INFO] Task started: HMMsearch
[2024-01-25 19:41:40,946] [INFO] Running command: hmmsearch --tblout GCF_002902405.1_ASM290240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference/reference_markers.hmm GCF_002902405.1_ASM290240v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:41,178] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:41,179] [INFO] Found 6/6 markers.
[2024-01-25 19:41:41,202] [INFO] Query marker FASTA was written to GCF_002902405.1_ASM290240v1_genomic.fna/markers.fasta
[2024-01-25 19:41:41,203] [INFO] Task started: Blastn
[2024-01-25 19:41:41,203] [INFO] Running command: blastn -query GCF_002902405.1_ASM290240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference/reference_markers.fasta -out GCF_002902405.1_ASM290240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:41,801] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:41,803] [INFO] Selected 10 target genomes.
[2024-01-25 19:41:41,803] [INFO] Target genome list was writen to GCF_002902405.1_ASM290240v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:41,812] [INFO] Task started: fastANI
[2024-01-25 19:41:41,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg03daf248-c769-4125-ab04-1124565f2f17/GCF_002902405.1_ASM290240v1_genomic.fna.gz --refList GCF_002902405.1_ASM290240v1_genomic.fna/target_genomes.txt --output GCF_002902405.1_ASM290240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:48,148] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:48,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:48,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:48,155] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:41:48,155] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:41:48,155] [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 schweitzeri	strain=DSM 28300	GCA_002902405.1	1654388	1654388	type	True	100.0	889	894	95	conclusive
Staphylococcus schweitzeri	strain=NCTC13712	GCA_900636685.1	1654388	1654388	type	True	99.9869	891	894	95	conclusive
Staphylococcus schweitzeri	strain=DSM 28300	GCA_014877095.1	1654388	1654388	type	True	99.9788	880	894	95	conclusive
Staphylococcus argenteus	strain=DSM 28299	GCA_014877305.1	985002	985002	type	True	92.8555	819	894	95	below_threshold
Staphylococcus argenteus	strain=MSHR1132	GCA_000236925.1	985002	985002	type	True	92.844	823	894	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	90.1946	813	894	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	90.1768	808	894	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.2171	304	894	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	78.2334	254	894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:48,157] [INFO] DFAST Taxonomy check result was written to GCF_002902405.1_ASM290240v1_genomic.fna/tc_result.tsv
[2024-01-25 19:41:48,157] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:48,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:48,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference/checkm_data
[2024-01-25 19:41:48,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:48,194] [INFO] Task started: CheckM
[2024-01-25 19:41:48,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902405.1_ASM290240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902405.1_ASM290240v1_genomic.fna/checkm_input GCF_002902405.1_ASM290240v1_genomic.fna/checkm_result
[2024-01-25 19:42:07,467] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:07,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:07,510] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:07,510] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:07,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902405.1_ASM290240v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:07,512] [INFO] Task started: Blastn
[2024-01-25 19:42:07,512] [INFO] Running command: blastn -query GCF_002902405.1_ASM290240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d8164c6-6af7-4a54-ba41-7ce6c553e5b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902405.1_ASM290240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:08,286] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:08,292] [INFO] Selected 8 target genomes.
[2024-01-25 19:42:08,292] [INFO] Target genome list was writen to GCF_002902405.1_ASM290240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:08,298] [INFO] Task started: fastANI
[2024-01-25 19:42:08,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg03daf248-c769-4125-ab04-1124565f2f17/GCF_002902405.1_ASM290240v1_genomic.fna.gz --refList GCF_002902405.1_ASM290240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902405.1_ASM290240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:13,648] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:13,655] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:13,655] [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_002902405.1	s__Staphylococcus schweitzeri	100.0	889	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	conclusive
GCF_015025035.1	s__Staphylococcus sp015025035	93.5582	823	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
GCF_000236925.1	s__Staphylococcus argenteus	92.8299	824	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	-
GCF_001027105.1	s__Staphylococcus aureus	90.1491	815	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.78	97.08	0.95	0.88	13059	-
GCF_002902085.1	s__Staphylococcus simiae	80.8001	490	894	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	80.7321	513	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.91	0.98	0.98	6	-
GCF_004785665.1	s__Staphylococcus pragensis	79.2593	310	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_002901845.1	s__Staphylococcus hominis	79.1302	289	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:13,656] [INFO] GTDB search result was written to GCF_002902405.1_ASM290240v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:13,657] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:13,659] [INFO] DFAST_QC result json was written to GCF_002902405.1_ASM290240v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:13,659] [INFO] DFAST_QC completed!
[2024-01-25 19:42:13,659] [INFO] Total running time: 0h0m38s