[2024-01-24 11:12:36,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference
[2024-01-24 11:12:38,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,663] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fdfbc91-3943-4ed4-8276-1caa3555be81/GCF_004359525.2_ASM435952v2_genomic.fna.gz | prodigal -d GCF_004359525.2_ASM435952v2_genomic.fna/cds.fna -a GCF_004359525.2_ASM435952v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:43,412] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:43,412] [INFO] Task started: HMMsearch
[2024-01-24 11:12:43,412] [INFO] Running command: hmmsearch --tblout GCF_004359525.2_ASM435952v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference/reference_markers.hmm GCF_004359525.2_ASM435952v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:43,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:43,603] [INFO] Found 6/6 markers.
[2024-01-24 11:12:43,624] [INFO] Query marker FASTA was written to GCF_004359525.2_ASM435952v2_genomic.fna/markers.fasta
[2024-01-24 11:12:43,625] [INFO] Task started: Blastn
[2024-01-24 11:12:43,625] [INFO] Running command: blastn -query GCF_004359525.2_ASM435952v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference/reference_markers.fasta -out GCF_004359525.2_ASM435952v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:44,199] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:44,202] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:44,202] [INFO] Target genome list was writen to GCF_004359525.2_ASM435952v2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:44,309] [INFO] Task started: fastANI
[2024-01-24 11:12:44,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fdfbc91-3943-4ed4-8276-1caa3555be81/GCF_004359525.2_ASM435952v2_genomic.fna.gz --refList GCF_004359525.2_ASM435952v2_genomic.fna/target_genomes.txt --output GCF_004359525.2_ASM435952v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:50,760] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:50,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:50,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:50,768] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:50,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:50,768] [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 equipercicus	strain=ATCC 51831	GCA_004359525.2	69967	69967	type	True	100.0	688	689	95	conclusive
Macrococcus lamae	strain=CCM4815	GCA_004359545.1	198484	198484	type	True	80.8639	401	689	95	below_threshold
Macrococcus carouselicus	strain=ATCC 51828	GCA_004359515.1	69969	69969	type	True	80.5601	230	689	95	below_threshold
Macrococcus bovicus	strain=ATCC 51825	GCA_004359575.1	69968	69968	type	True	79.4875	211	689	95	below_threshold
Macrococcus hajekii	strain=CCM4809	GCA_004359505.1	198482	198482	type	True	79.2298	196	689	95	below_threshold
Macrococcus hajekii	strain=CCM 4809	GCA_014634985.1	198482	198482	type	True	79.2229	197	689	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	79.1741	99	689	95	below_threshold
Macrococcus brunensis	strain=CCM4811	GCA_004359615.1	198483	198483	type	True	79.0263	216	689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:50,769] [INFO] DFAST Taxonomy check result was written to GCF_004359525.2_ASM435952v2_genomic.fna/tc_result.tsv
[2024-01-24 11:12:50,770] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:50,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:50,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference/checkm_data
[2024-01-24 11:12:50,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:50,795] [INFO] Task started: CheckM
[2024-01-24 11:12:50,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004359525.2_ASM435952v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004359525.2_ASM435952v2_genomic.fna/checkm_input GCF_004359525.2_ASM435952v2_genomic.fna/checkm_result
[2024-01-24 11:13:11,618] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:11,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:11,641] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:11,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:11,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004359525.2_ASM435952v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:11,642] [INFO] Task started: Blastn
[2024-01-24 11:13:11,642] [INFO] Running command: blastn -query GCF_004359525.2_ASM435952v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a7f6fad-cffb-4899-9f04-20fd145f36dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004359525.2_ASM435952v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:12,427] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:12,430] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:12,430] [INFO] Target genome list was writen to GCF_004359525.2_ASM435952v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:12,444] [INFO] Task started: fastANI
[2024-01-24 11:13:12,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fdfbc91-3943-4ed4-8276-1caa3555be81/GCF_004359525.2_ASM435952v2_genomic.fna.gz --refList GCF_004359525.2_ASM435952v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004359525.2_ASM435952v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:20,485] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,493] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:20,493] [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_004359525.2	s__Macrococcus equipercicus	100.0	688	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002438305.1	s__Macrococcus sp002438305	80.884	297	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	98.53	98.53	0.76	0.76	2	-
GCF_004359545.1	s__Macrococcus lamae	80.8833	401	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359515.1	s__Macrococcus carouselicus	80.5601	230	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359575.1	s__Macrococcus bovicus	79.4873	211	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359505.1	s__Macrococcus hajekii	79.2429	195	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004359615.1	s__Macrococcus brunensis	79.006	217	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259675.1	s__Macrococcus_B bohemicus	78.6569	102	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.03	97.95	0.86	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,495] [INFO] GTDB search result was written to GCF_004359525.2_ASM435952v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:20,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:20,498] [INFO] DFAST_QC result json was written to GCF_004359525.2_ASM435952v2_genomic.fna/dqc_result.json
[2024-01-24 11:13:20,498] [INFO] DFAST_QC completed!
[2024-01-24 11:13:20,498] [INFO] Total running time: 0h0m44s