[2024-01-24 11:26:54,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference
[2024-01-24 11:26:58,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,225] [INFO] Running command: gunzip -c /var/lib/cwl/stga2a1d79e-64b9-4263-89ec-11ffaaf2718e/GCF_004359545.1_ASM435954v1_genomic.fna.gz | prodigal -d GCF_004359545.1_ASM435954v1_genomic.fna/cds.fna -a GCF_004359545.1_ASM435954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:02,625] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:02,625] [INFO] Task started: HMMsearch
[2024-01-24 11:27:02,626] [INFO] Running command: hmmsearch --tblout GCF_004359545.1_ASM435954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference/reference_markers.hmm GCF_004359545.1_ASM435954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:02,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:02,867] [INFO] Found 6/6 markers.
[2024-01-24 11:27:02,890] [INFO] Query marker FASTA was written to GCF_004359545.1_ASM435954v1_genomic.fna/markers.fasta
[2024-01-24 11:27:02,891] [INFO] Task started: Blastn
[2024-01-24 11:27:02,891] [INFO] Running command: blastn -query GCF_004359545.1_ASM435954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference/reference_markers.fasta -out GCF_004359545.1_ASM435954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:03,725] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:03,728] [INFO] Selected 22 target genomes.
[2024-01-24 11:27:03,728] [INFO] Target genome list was writen to GCF_004359545.1_ASM435954v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:03,821] [INFO] Task started: fastANI
[2024-01-24 11:27:03,822] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a1d79e-64b9-4263-89ec-11ffaaf2718e/GCF_004359545.1_ASM435954v1_genomic.fna.gz --refList GCF_004359545.1_ASM435954v1_genomic.fna/target_genomes.txt --output GCF_004359545.1_ASM435954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:14,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:14,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:14,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:14,220] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:14,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:14,220] [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 lamae	strain=CCM4815	GCA_004359545.1	198484	198484	type	True	100.0	655	655	95	conclusive
Macrococcus equipercicus	strain=ATCC 51831	GCA_004359525.2	69967	69967	type	True	81.0011	394	655	95	below_threshold
Macrococcus carouselicus	strain=ATCC 51828	GCA_004359515.1	69969	69969	type	True	79.2063	181	655	95	below_threshold
Macrococcus brunensis	strain=CCM4811	GCA_004359615.1	198483	198483	type	True	79.1392	194	655	95	below_threshold
Macrococcus hajekii	strain=CCM 4809	GCA_014634985.1	198482	198482	type	True	78.5722	190	655	95	below_threshold
Macrococcus hajekii	strain=CCM4809	GCA_004359505.1	198482	198482	type	True	78.5412	195	655	95	below_threshold
Staphylococcus carnosus	strain=FDAARGOS_883	GCA_016028275.1	1281	1281	type	True	77.8413	55	655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,222] [INFO] DFAST Taxonomy check result was written to GCF_004359545.1_ASM435954v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:14,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:14,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:14,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference/checkm_data
[2024-01-24 11:27:14,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:14,247] [INFO] Task started: CheckM
[2024-01-24 11:27:14,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004359545.1_ASM435954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004359545.1_ASM435954v1_genomic.fna/checkm_input GCF_004359545.1_ASM435954v1_genomic.fna/checkm_result
[2024-01-24 11:27:34,936] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:34,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,959] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:34,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:34,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004359545.1_ASM435954v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:34,960] [INFO] Task started: Blastn
[2024-01-24 11:27:34,960] [INFO] Running command: blastn -query GCF_004359545.1_ASM435954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaac4f68-94d3-4bf3-ac9b-fadaf53c9962/dqc_reference/reference_markers_gtdb.fasta -out GCF_004359545.1_ASM435954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:35,690] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:35,694] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:35,694] [INFO] Target genome list was writen to GCF_004359545.1_ASM435954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:35,734] [INFO] Task started: fastANI
[2024-01-24 11:27:35,734] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a1d79e-64b9-4263-89ec-11ffaaf2718e/GCF_004359545.1_ASM435954v1_genomic.fna.gz --refList GCF_004359545.1_ASM435954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004359545.1_ASM435954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:43,824] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:43,838] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:43,839] [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_004359545.1	s__Macrococcus lamae	100.0	655	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004359525.2	s__Macrococcus equipercicus	81.0011	394	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438305.1	s__Macrococcus sp002438305	79.6162	278	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	98.53	98.53	0.76	0.76	2	-
GCF_004359515.1	s__Macrococcus carouselicus	79.1802	182	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359615.1	s__Macrococcus brunensis	79.1495	196	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259695.1	s__Macrococcus_B epidermidis	78.7552	116	655	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_003259675.1	s__Macrococcus_B bohemicus	78.7473	118	655	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_004117835.1	s__Macrococcus_B sp004117835	78.5907	105	655	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_004359505.1	s__Macrococcus hajekii	78.5412	195	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002742385.2	s__Macrococcus_B goetzii	78.223	125	655	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_900458435.1	s__Staphylococcus carnosus	77.8663	51	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,840] [INFO] GTDB search result was written to GCF_004359545.1_ASM435954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:43,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:43,844] [INFO] DFAST_QC result json was written to GCF_004359545.1_ASM435954v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:43,845] [INFO] DFAST_QC completed!
[2024-01-24 11:27:43,845] [INFO] Total running time: 0h0m50s