[2024-01-24 14:19:15,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference
[2024-01-24 14:19:16,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,620] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg91c8cf5d-9516-4eed-a2a6-4976aa299085/GCF_002901705.1_ASM290170v1_genomic.fna.gz | prodigal -d GCF_002901705.1_ASM290170v1_genomic.fna/cds.fna -a GCF_002901705.1_ASM290170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:21,515] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:21,515] [INFO] Task started: HMMsearch
[2024-01-24 14:19:21,515] [INFO] Running command: hmmsearch --tblout GCF_002901705.1_ASM290170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference/reference_markers.hmm GCF_002901705.1_ASM290170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:21,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:21,811] [INFO] Found 6/6 markers.
[2024-01-24 14:19:21,839] [INFO] Query marker FASTA was written to GCF_002901705.1_ASM290170v1_genomic.fna/markers.fasta
[2024-01-24 14:19:21,840] [INFO] Task started: Blastn
[2024-01-24 14:19:21,840] [INFO] Running command: blastn -query GCF_002901705.1_ASM290170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference/reference_markers.fasta -out GCF_002901705.1_ASM290170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:22,509] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:22,512] [INFO] Selected 20 target genomes.
[2024-01-24 14:19:22,513] [INFO] Target genome list was writen to GCF_002901705.1_ASM290170v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:22,524] [INFO] Task started: fastANI
[2024-01-24 14:19:22,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg91c8cf5d-9516-4eed-a2a6-4976aa299085/GCF_002901705.1_ASM290170v1_genomic.fna.gz --refList GCF_002901705.1_ASM290170v1_genomic.fna/target_genomes.txt --output GCF_002901705.1_ASM290170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:31,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:31,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:31,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:31,746] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:31,746] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:31,746] [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 lugdunensis	strain=NCTC 12217	GCA_002901705.1	28035	28035	type	True	100.0	834	835	95	conclusive
Staphylococcus lugdunensis	strain=NCTC12217	GCA_900478255.1	28035	28035	type	True	99.9886	834	835	95	conclusive
Staphylococcus petrasii	strain=CCM 8418	GCA_004684865.1	1276936	1276936	type	True	79.3773	348	835	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	79.3727	350	835	95	below_threshold
Staphylococcus warneri	strain=NCTC 11044	GCA_002901765.1	1292	1292	type	True	79.366	296	835	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	79.3598	344	835	95	below_threshold
Staphylococcus warneri	strain=NCTC11044	GCA_900636385.1	1292	1292	type	True	79.3212	299	835	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.1921	377	835	95	below_threshold
Staphylococcus haemolyticus	strain=ATCC 29970	GCA_006094395.1	1283	1283	type	True	79.1656	329	835	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC11042	GCA_900458595.1	1283	1283	type	True	79.1251	326	835	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	79.1097	325	835	95	below_threshold
Staphylococcus pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	78.8719	320	835	95	below_threshold
Staphylococcus schweitzeri	strain=DSM 28300	GCA_014877095.1	1654388	1654388	type	True	78.8172	288	835	95	below_threshold
Staphylococcus schweitzeri	strain=NCTC13712	GCA_900636685.1	1654388	1654388	type	True	78.815	287	835	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.6135	299	835	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.6042	298	835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:31,748] [INFO] DFAST Taxonomy check result was written to GCF_002901705.1_ASM290170v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:31,749] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:31,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:31,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference/checkm_data
[2024-01-24 14:19:31,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:31,779] [INFO] Task started: CheckM
[2024-01-24 14:19:31,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002901705.1_ASM290170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002901705.1_ASM290170v1_genomic.fna/checkm_input GCF_002901705.1_ASM290170v1_genomic.fna/checkm_result
[2024-01-24 14:19:58,468] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:58,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:58,585] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:58,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:58,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002901705.1_ASM290170v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:58,586] [INFO] Task started: Blastn
[2024-01-24 14:19:58,587] [INFO] Running command: blastn -query GCF_002901705.1_ASM290170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a3bf2b3-b7d0-4a9b-b4aa-3a04cdaae451/dqc_reference/reference_markers_gtdb.fasta -out GCF_002901705.1_ASM290170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:59,867] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:59,870] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:59,871] [INFO] Target genome list was writen to GCF_002901705.1_ASM290170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:59,881] [INFO] Task started: fastANI
[2024-01-24 14:19:59,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg91c8cf5d-9516-4eed-a2a6-4976aa299085/GCF_002901705.1_ASM290170v1_genomic.fna.gz --refList GCF_002901705.1_ASM290170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002901705.1_ASM290170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:13,684] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:13,704] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:13,705] [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_002901705.1	s__Staphylococcus lugdunensis	100.0	834	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.51	99.34	0.98	0.96	70	conclusive
GCF_003035445.1	s__Staphylococcus devriesei_A	79.4048	322	835	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	79.4045	331	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902565.1	s__Staphylococcus petrasii	79.3807	342	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_900636385.1	s__Staphylococcus warneri	79.3212	299	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_001224225.1	s__Staphylococcus borealis	79.3	336	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002902625.1	s__Staphylococcus devriesei	79.2281	293	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_004785665.1	s__Staphylococcus pragensis	79.2135	352	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_006094395.1	s__Staphylococcus haemolyticus	79.1512	330	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_003491325.1	s__Staphylococcus warneri_A	78.964	319	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.8507	321	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002902405.1	s__Staphylococcus schweitzeri	78.8038	284	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_002902725.1	s__Staphylococcus caprae	78.6189	322	835	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:13,707] [INFO] GTDB search result was written to GCF_002901705.1_ASM290170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:13,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:13,716] [INFO] DFAST_QC result json was written to GCF_002901705.1_ASM290170v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:13,716] [INFO] DFAST_QC completed!
[2024-01-24 14:20:13,716] [INFO] Total running time: 0h0m58s