[2024-01-24 13:13:23,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference
[2024-01-24 13:13:25,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,057] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e526b07-d2ce-4a5e-8422-34b2e749baf2/GCF_003968885.1_ASM396888v1_genomic.fna.gz | prodigal -d GCF_003968885.1_ASM396888v1_genomic.fna/cds.fna -a GCF_003968885.1_ASM396888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:28,919] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:28,919] [INFO] Task started: HMMsearch
[2024-01-24 13:13:28,919] [INFO] Running command: hmmsearch --tblout GCF_003968885.1_ASM396888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference/reference_markers.hmm GCF_003968885.1_ASM396888v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:29,222] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:29,223] [INFO] Found 6/6 markers.
[2024-01-24 13:13:29,248] [INFO] Query marker FASTA was written to GCF_003968885.1_ASM396888v1_genomic.fna/markers.fasta
[2024-01-24 13:13:29,248] [INFO] Task started: Blastn
[2024-01-24 13:13:29,248] [INFO] Running command: blastn -query GCF_003968885.1_ASM396888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference/reference_markers.fasta -out GCF_003968885.1_ASM396888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:29,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:29,928] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:29,929] [INFO] Target genome list was writen to GCF_003968885.1_ASM396888v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:29,953] [INFO] Task started: fastANI
[2024-01-24 13:13:29,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e526b07-d2ce-4a5e-8422-34b2e749baf2/GCF_003968885.1_ASM396888v1_genomic.fna.gz --refList GCF_003968885.1_ASM396888v1_genomic.fna/target_genomes.txt --output GCF_003968885.1_ASM396888v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:39,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:39,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:39,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:39,077] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:13:39,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:39,077] [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 saccharolyticus	strain=NCTC 11807	GCA_003968885.1	33028	33028	type	True	100.0	734	740	95	conclusive
Staphylococcus saccharolyticus	strain=NCTC11807	GCA_900458815.1	33028	33028	type	True	99.9877	739	740	95	conclusive
Staphylococcus saccharolyticus	strain=FDAARGOS_1074	GCA_016127715.1	33028	33028	type	True	99.9877	734	740	95	conclusive
Staphylococcus caprae	strain=NCTC 12196	GCA_002902725.1	29380	29380	type	True	81.5516	496	740	95	below_threshold
Staphylococcus caprae	strain=NCTC12196	GCA_900458385.1	29380	29380	type	True	81.5331	504	740	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=NCTC 11045	GCA_002902325.1	72758	29388	type	True	81.5039	494	740	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	81.4562	502	740	95	below_threshold
Staphylococcus capitis subsp. urealyticus	strain=DSM 6717	GCA_002901925.1	74703	29388	type	True	81.449	481	740	95	below_threshold
Staphylococcus capitis	strain=NCTC11045	GCA_901482635.1	29388	29388	type	True	81.4365	502	740	95	below_threshold
Staphylococcus epidermidis	strain=ATCC 14990	GCA_006094375.1	1282	1282	type	True	81.3303	508	740	95	below_threshold
Staphylococcus epidermidis	strain=NCTC11047	GCA_900458605.1	1282	1282	type	True	81.2436	505	740	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.0861	311	740	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.9525	291	740	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.8546	295	740	95	below_threshold
Staphylococcus caledonicus	strain=H8/1	GCA_016238465.1	2741333	2741333	type	True	78.7826	320	740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:39,085] [INFO] DFAST Taxonomy check result was written to GCF_003968885.1_ASM396888v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:39,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:39,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:39,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference/checkm_data
[2024-01-24 13:13:39,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:39,118] [INFO] Task started: CheckM
[2024-01-24 13:13:39,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003968885.1_ASM396888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003968885.1_ASM396888v1_genomic.fna/checkm_input GCF_003968885.1_ASM396888v1_genomic.fna/checkm_result
[2024-01-24 13:13:59,802] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:59,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:59,824] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:59,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:59,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003968885.1_ASM396888v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:59,825] [INFO] Task started: Blastn
[2024-01-24 13:13:59,825] [INFO] Running command: blastn -query GCF_003968885.1_ASM396888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6606650-cd38-4eee-a71d-bb14e4741688/dqc_reference/reference_markers_gtdb.fasta -out GCF_003968885.1_ASM396888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,680] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,683] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:00,684] [INFO] Target genome list was writen to GCF_003968885.1_ASM396888v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:00,697] [INFO] Task started: fastANI
[2024-01-24 13:14:00,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e526b07-d2ce-4a5e-8422-34b2e749baf2/GCF_003968885.1_ASM396888v1_genomic.fna.gz --refList GCF_003968885.1_ASM396888v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003968885.1_ASM396888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:05,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:05,948] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:05,948] [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_900458815.1	s__Staphylococcus saccharolyticus	99.9877	739	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.11	97.94	0.98	0.95	15	conclusive
GCF_002902725.1	s__Staphylococcus caprae	81.5376	497	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_002902325.1	s__Staphylococcus capitis	81.4894	495	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_006742205.1	s__Staphylococcus epidermidis	81.2244	511	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.01	96.59	0.94	0.83	1079	-
GCF_003970495.1	s__Staphylococcus pasteuri	79.7869	371	740	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	79.5805	366	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_004785665.1	s__Staphylococcus pragensis	79.2623	324	740	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	79.1455	309	740	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	78.8776	312	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_002901705.1	s__Staphylococcus lugdunensis	78.5405	283	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.51	99.34	0.98	0.96	70	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:05,950] [INFO] GTDB search result was written to GCF_003968885.1_ASM396888v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:05,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:05,953] [INFO] DFAST_QC result json was written to GCF_003968885.1_ASM396888v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:05,954] [INFO] DFAST_QC completed!
[2024-01-24 13:14:05,954] [INFO] Total running time: 0h0m42s