[2024-01-25 19:54:20,479] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:20,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:20,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference
[2024-01-25 19:54:21,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:21,612] [INFO] Task started: Prodigal
[2024-01-25 19:54:21,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e22ba66-9f75-4f00-9cfc-d84af1286ec9/GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/cds.fna -a GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:28,050] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:28,051] [INFO] Task started: HMMsearch
[2024-01-25 19:54:28,051] [INFO] Running command: hmmsearch --tblout GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference/reference_markers.hmm GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:28,250] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:28,251] [INFO] Found 6/6 markers.
[2024-01-25 19:54:28,274] [INFO] Query marker FASTA was written to GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:54:28,274] [INFO] Task started: Blastn
[2024-01-25 19:54:28,274] [INFO] Running command: blastn -query GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference/reference_markers.fasta -out GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:28,828] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:28,830] [INFO] Selected 13 target genomes.
[2024-01-25 19:54:28,831] [INFO] Target genome list was writen to GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:54:28,858] [INFO] Task started: fastANI
[2024-01-25 19:54:28,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e22ba66-9f75-4f00-9cfc-d84af1286ec9/GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna.gz --refList GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:35,478] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:35,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:35,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:35,485] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:35,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:35,486] [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
Salinicoccus kekensis	strain=DSM 23173	GCA_900220995.1	714307	714307	type	True	100.0	864	864	95	conclusive
Salinicoccus alkaliphilus	strain=DSM 16010	GCA_900142805.1	148453	148453	type	True	83.0509	661	864	95	below_threshold
Salinicoccus qingdaonensis	strain=CGMCC 1.8895	GCA_900101075.1	576118	576118	type	True	79.0925	389	864	95	below_threshold
Salinicoccus sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	77.473	142	864	95	below_threshold
Salinicoccus carnicancri	strain=Crm	GCA_000330705.1	558170	558170	type	True	77.4143	125	864	95	below_threshold
Jeotgalicoccus saudimassiliensis	strain=13MG44_air	GCA_000756715.2	1461582	1461582	type	True	77.0551	73	864	95	below_threshold
Salinicoccus halodurans	strain=CGMCC 1.6501	GCA_900114445.1	407035	407035	type	True	77.0353	143	864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:35,487] [INFO] DFAST Taxonomy check result was written to GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:54:35,487] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:35,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:35,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference/checkm_data
[2024-01-25 19:54:35,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:35,519] [INFO] Task started: CheckM
[2024-01-25 19:54:35,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/checkm_input GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:54:59,771] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:59,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:59,787] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:59,788] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:59,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:54:59,788] [INFO] Task started: Blastn
[2024-01-25 19:54:59,788] [INFO] Running command: blastn -query GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fade88a-4061-42f7-b208-de687ab48ed3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:00,624] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:00,637] [INFO] Selected 15 target genomes.
[2024-01-25 19:55:00,637] [INFO] Target genome list was writen to GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:00,654] [INFO] Task started: fastANI
[2024-01-25 19:55:00,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e22ba66-9f75-4f00-9cfc-d84af1286ec9/GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna.gz --refList GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:08,365] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:08,371] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:08,371] [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_900220995.1	s__Salinicoccus kekensis	100.0	864	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142805.1	s__Salinicoccus alkaliphilus	83.0444	661	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101075.1	s__Salinicoccus qingdaonensis	79.1021	389	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360325.1	s__Salinicoccus merdavium	78.7377	304	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	99.13	99.13	0.85	0.85	2	-
GCF_001265075.1	s__Salinicoccus sp001265075	78.7233	385	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713705.1	s__Salinicoccus cyprini	77.1989	149	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831115.1	s__Salinicoccus hispanicus	76.9683	150	864	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:08,372] [INFO] GTDB search result was written to GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:08,373] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:08,375] [INFO] DFAST_QC result json was written to GCF_900220995.1_IMG-taxon_2740891890_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:55:08,375] [INFO] DFAST_QC completed!
[2024-01-25 19:55:08,375] [INFO] Total running time: 0h0m48s