[2024-01-24 13:22:42,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:42,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:42,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference
[2024-01-24 13:22:43,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:43,676] [INFO] Task started: Prodigal
[2024-01-24 13:22:43,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg82aad5b4-a545-4f42-b89e-dd96ce2ca5b5/GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/cds.fna -a GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:50,839] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:50,840] [INFO] Task started: HMMsearch
[2024-01-24 13:22:50,840] [INFO] Running command: hmmsearch --tblout GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference/reference_markers.hmm GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:51,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:51,134] [INFO] Found 6/6 markers.
[2024-01-24 13:22:51,161] [INFO] Query marker FASTA was written to GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:51,162] [INFO] Task started: Blastn
[2024-01-24 13:22:51,162] [INFO] Running command: blastn -query GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference/reference_markers.fasta -out GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:51,870] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:51,873] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:51,874] [INFO] Target genome list was writen to GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:51,927] [INFO] Task started: fastANI
[2024-01-24 13:22:51,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg82aad5b4-a545-4f42-b89e-dd96ce2ca5b5/GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna.gz --refList GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:01,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:01,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:01,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:01,546] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:01,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:01,547] [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 alkaliphilus	strain=DSM 16010	GCA_900142805.1	148453	148453	type	True	100.0	825	826	95	conclusive
Salinicoccus kekensis	strain=DSM 23173	GCA_900220995.1	714307	714307	type	True	82.9894	667	826	95	below_threshold
Salinicoccus qingdaonensis	strain=CGMCC 1.8895	GCA_900101075.1	576118	576118	type	True	79.1051	363	826	95	below_threshold
Salinicoccus luteus	strain=DSM 17002	GCA_000712035.1	367840	367840	type	True	77.3853	144	826	95	below_threshold
Salinicoccus roseus	strain=DSM 5351	GCA_003814515.1	45670	45670	type	True	77.3828	150	826	95	below_threshold
Salinicoccus roseus	strain=CCM 3516	GCA_014634945.1	45670	45670	type	True	77.3381	149	826	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	77.0674	123	826	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	77.0328	114	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,548] [INFO] DFAST Taxonomy check result was written to GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:23:01,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:01,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:01,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference/checkm_data
[2024-01-24 13:23:01,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:01,590] [INFO] Task started: CheckM
[2024-01-24 13:23:01,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/checkm_input GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:29,803] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:29,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:29,827] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:29,828] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:29,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:29,829] [INFO] Task started: Blastn
[2024-01-24 13:23:29,829] [INFO] Running command: blastn -query GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87d6f422-fbfa-4aac-ab7b-58f49ea8bcb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:30,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:30,657] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:30,657] [INFO] Target genome list was writen to GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:30,672] [INFO] Task started: fastANI
[2024-01-24 13:23:30,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg82aad5b4-a545-4f42-b89e-dd96ce2ca5b5/GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna.gz --refList GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:36,816] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:36,826] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:36,827] [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_900142805.1	s__Salinicoccus alkaliphilus	100.0	825	826	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_900220995.1	s__Salinicoccus kekensis	82.9908	666	826	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	79.1051	363	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001265075.1	s__Salinicoccus sp001265075	78.8132	355	826	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	78.4598	308	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	99.13	99.13	0.85	0.85	2	-
GCF_000712035.1	s__Salinicoccus luteus	77.3832	144	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814515.1	s__Salinicoccus roseus	77.3828	150	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	97.90	96.75	0.92	0.87	5	-
GCF_007713705.1	s__Salinicoccus cyprini	77.0662	123	826	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	77.0281	113	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,828] [INFO] GTDB search result was written to GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:36,829] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:36,833] [INFO] DFAST_QC result json was written to GCF_900142805.1_IMG-taxon_2582580728_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:36,833] [INFO] DFAST_QC completed!
[2024-01-24 13:23:36,833] [INFO] Total running time: 0h0m54s