[2024-01-25 20:16:50,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:50,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:50,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference
[2024-01-25 20:16:51,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:51,751] [INFO] Task started: Prodigal
[2024-01-25 20:16:51,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg6127f539-d5c3-4612-adc8-cc960edaa50e/GCF_002902665.1_ASM290266v1_genomic.fna.gz | prodigal -d GCF_002902665.1_ASM290266v1_genomic.fna/cds.fna -a GCF_002902665.1_ASM290266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:55,392] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:55,392] [INFO] Task started: HMMsearch
[2024-01-25 20:16:55,392] [INFO] Running command: hmmsearch --tblout GCF_002902665.1_ASM290266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference/reference_markers.hmm GCF_002902665.1_ASM290266v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:55,605] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:55,606] [INFO] Found 6/6 markers.
[2024-01-25 20:16:55,628] [INFO] Query marker FASTA was written to GCF_002902665.1_ASM290266v1_genomic.fna/markers.fasta
[2024-01-25 20:16:55,628] [INFO] Task started: Blastn
[2024-01-25 20:16:55,628] [INFO] Running command: blastn -query GCF_002902665.1_ASM290266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference/reference_markers.fasta -out GCF_002902665.1_ASM290266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:56,167] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:56,170] [INFO] Selected 10 target genomes.
[2024-01-25 20:16:56,171] [INFO] Target genome list was writen to GCF_002902665.1_ASM290266v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:56,174] [INFO] Task started: fastANI
[2024-01-25 20:16:56,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg6127f539-d5c3-4612-adc8-cc960edaa50e/GCF_002902665.1_ASM290266v1_genomic.fna.gz --refList GCF_002902665.1_ASM290266v1_genomic.fna/target_genomes.txt --output GCF_002902665.1_ASM290266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:01,697] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:01,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:01,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:01,704] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:17:01,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:01,704] [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
Macrococcus caseolyticus	strain=DSM 20597	GCA_002902665.1	69966	69966	type	True	100.0	676	680	95	conclusive
Macrococcus caseolyticus	strain=FDAARGOS_868	GCA_016028795.1	69966	69966	type	True	99.9881	670	680	95	conclusive
Macrococcus caseolyticus subsp. caseolyticus	strain=CCM 3540	GCA_003259685.1	2233644	69966	type	True	99.9831	646	680	95	conclusive
Macrococcus caseolyticus subsp. hominis	strain=CCM 7927	GCA_002742395.2	1891096	69966	type	True	96.7262	574	680	95	conclusive
Macrococcus canis	strain=KM 45013	GCA_002119805.1	1855823	1855823	type	True	87.9554	563	680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:01,705] [INFO] DFAST Taxonomy check result was written to GCF_002902665.1_ASM290266v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:01,706] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:01,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:01,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference/checkm_data
[2024-01-25 20:17:01,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:01,730] [INFO] Task started: CheckM
[2024-01-25 20:17:01,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902665.1_ASM290266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902665.1_ASM290266v1_genomic.fna/checkm_input GCF_002902665.1_ASM290266v1_genomic.fna/checkm_result
[2024-01-25 20:17:18,874] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:18,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:18,927] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:18,927] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:18,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902665.1_ASM290266v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:18,928] [INFO] Task started: Blastn
[2024-01-25 20:17:18,928] [INFO] Running command: blastn -query GCF_002902665.1_ASM290266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2459208-016a-4a83-a95c-14368e0854bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902665.1_ASM290266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:19,682] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:19,687] [INFO] Selected 20 target genomes.
[2024-01-25 20:17:19,687] [INFO] Target genome list was writen to GCF_002902665.1_ASM290266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:19,707] [INFO] Task started: fastANI
[2024-01-25 20:17:19,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg6127f539-d5c3-4612-adc8-cc960edaa50e/GCF_002902665.1_ASM290266v1_genomic.fna.gz --refList GCF_002902665.1_ASM290266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902665.1_ASM290266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:28,035] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:28,045] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:28,045] [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_002902665.1	s__Macrococcus_B caseolyticus	100.0	676	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.20	96.60	0.90	0.84	54	conclusive
GCF_002119805.1	s__Macrococcus_B canis	87.9755	562	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	96.44	96.14	0.86	0.82	14	-
GCF_003259675.1	s__Macrococcus_B bohemicus	81.7806	278	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.03	97.95	0.86	0.85	5	-
GCF_003259695.1	s__Macrococcus_B epidermidis	80.4592	251	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	N/A	N/A	N/A	N/A	1	-
GCF_002742385.2	s__Macrococcus_B goetzii	80.1394	266	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	96.60	96.57	0.86	0.86	4	-
GCF_004359515.1	s__Macrococcus carouselicus	79.1549	90	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117835.1	s__Macrococcus_B sp004117835	79.0841	175	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236925.1	s__Staphylococcus argenteus	78.9111	61	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	-
GCF_010365305.1	s__Staphylococcus sp010365305	78.8162	62	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359615.1	s__Macrococcus brunensis	78.5812	119	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901825.1	s__Mammaliicoccus sciuri	78.3151	101	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_002902755.1	s__Mammaliicoccus lentus	78.039	75	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.03	97.66	0.94	0.90	21	-
GCF_003491325.1	s__Staphylococcus warneri_A	78.0229	67	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902725.1	s__Staphylococcus caprae	78.0166	74	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_002901845.1	s__Staphylococcus hominis	77.8916	70	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
GCF_002902325.1	s__Staphylococcus capitis	77.6155	70	680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:28,047] [INFO] GTDB search result was written to GCF_002902665.1_ASM290266v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:28,047] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:28,052] [INFO] DFAST_QC result json was written to GCF_002902665.1_ASM290266v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:28,052] [INFO] DFAST_QC completed!
[2024-01-25 20:17:28,052] [INFO] Total running time: 0h0m37s