[2024-01-25 20:17:35,742] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:35,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:35,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference
[2024-01-25 20:17:36,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:36,863] [INFO] Task started: Prodigal
[2024-01-25 20:17:36,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg01cd5e72-15d3-4e3a-a190-755771c004a2/GCF_002902325.1_ASM290232v1_genomic.fna.gz | prodigal -d GCF_002902325.1_ASM290232v1_genomic.fna/cds.fna -a GCF_002902325.1_ASM290232v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:40,551] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:40,552] [INFO] Task started: HMMsearch
[2024-01-25 20:17:40,552] [INFO] Running command: hmmsearch --tblout GCF_002902325.1_ASM290232v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference/reference_markers.hmm GCF_002902325.1_ASM290232v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:40,761] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:40,762] [INFO] Found 6/6 markers.
[2024-01-25 20:17:40,789] [INFO] Query marker FASTA was written to GCF_002902325.1_ASM290232v1_genomic.fna/markers.fasta
[2024-01-25 20:17:40,790] [INFO] Task started: Blastn
[2024-01-25 20:17:40,790] [INFO] Running command: blastn -query GCF_002902325.1_ASM290232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference/reference_markers.fasta -out GCF_002902325.1_ASM290232v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:41,362] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:41,364] [INFO] Selected 9 target genomes.
[2024-01-25 20:17:41,365] [INFO] Target genome list was writen to GCF_002902325.1_ASM290232v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:41,371] [INFO] Task started: fastANI
[2024-01-25 20:17:41,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg01cd5e72-15d3-4e3a-a190-755771c004a2/GCF_002902325.1_ASM290232v1_genomic.fna.gz --refList GCF_002902325.1_ASM290232v1_genomic.fna/target_genomes.txt --output GCF_002902325.1_ASM290232v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:46,200] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:46,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:46,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:46,206] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 20:17:46,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:46,206] [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 capitis subsp. capitis	strain=NCTC 11045	GCA_002902325.1	72758	29388	type	True	100.0	790	792	95	conclusive
Staphylococcus capitis	strain=CCM 2734	GCA_014635765.1	29388	29388	type	True	99.9879	790	792	95	conclusive
Staphylococcus capitis	strain=NCTC11045	GCA_901482635.1	29388	29388	type	True	99.9867	792	792	95	conclusive
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	99.9844	792	792	95	conclusive
Staphylococcus capitis subsp. urealyticus	strain=DSM 6717	GCA_002901925.1	74703	29388	type	True	96.58	715	792	95	conclusive
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.4959	379	792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:46,207] [INFO] DFAST Taxonomy check result was written to GCF_002902325.1_ASM290232v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:46,208] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:46,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:46,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference/checkm_data
[2024-01-25 20:17:46,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:46,236] [INFO] Task started: CheckM
[2024-01-25 20:17:46,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902325.1_ASM290232v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902325.1_ASM290232v1_genomic.fna/checkm_input GCF_002902325.1_ASM290232v1_genomic.fna/checkm_result
[2024-01-25 20:18:03,468] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:03,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:03,496] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:03,496] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:03,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902325.1_ASM290232v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:03,496] [INFO] Task started: Blastn
[2024-01-25 20:18:03,496] [INFO] Running command: blastn -query GCF_002902325.1_ASM290232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb1ab07-d66d-4484-a421-7363604ced71/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902325.1_ASM290232v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:04,350] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:04,354] [INFO] Selected 12 target genomes.
[2024-01-25 20:18:04,355] [INFO] Target genome list was writen to GCF_002902325.1_ASM290232v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:04,362] [INFO] Task started: fastANI
[2024-01-25 20:18:04,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg01cd5e72-15d3-4e3a-a190-755771c004a2/GCF_002902325.1_ASM290232v1_genomic.fna.gz --refList GCF_002902325.1_ASM290232v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902325.1_ASM290232v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:10,653] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:10,662] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:10,662] [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_002902325.1	s__Staphylococcus capitis	100.0	790	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	conclusive
GCF_002902725.1	s__Staphylococcus caprae	84.3107	628	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_900458815.1	s__Staphylococcus saccharolyticus	81.4861	535	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.11	97.94	0.98	0.95	15	-
GCF_006742205.1	s__Staphylococcus epidermidis	80.5373	495	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.01	96.59	0.94	0.83	1079	-
GCF_900636385.1	s__Staphylococcus warneri	80.3569	438	792	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	80.2913	433	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_003491325.1	s__Staphylococcus warneri_A	80.2232	441	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_004785665.1	s__Staphylococcus pragensis	79.9436	378	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_002902565.1	s__Staphylococcus petrasii	79.9334	381	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_003035445.1	s__Staphylococcus devriesei_A	79.7546	354	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCA_002902575.1	s__Staphylococcus croceilyticus	79.6419	378	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_015025035.1	s__Staphylococcus sp015025035	79.4238	333	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:10,663] [INFO] GTDB search result was written to GCF_002902325.1_ASM290232v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:10,664] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:10,667] [INFO] DFAST_QC result json was written to GCF_002902325.1_ASM290232v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:10,667] [INFO] DFAST_QC completed!
[2024-01-25 20:18:10,667] [INFO] Total running time: 0h0m35s