[2024-01-24 13:25:29,806] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference
[2024-01-24 13:25:31,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,126] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cbb86fd-bf2d-4d6a-b279-35d349522654/GCF_000330705.1_Crm_genomic.fna.gz | prodigal -d GCF_000330705.1_Crm_genomic.fna/cds.fna -a GCF_000330705.1_Crm_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:38,646] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:38,646] [INFO] Task started: HMMsearch
[2024-01-24 13:25:38,646] [INFO] Running command: hmmsearch --tblout GCF_000330705.1_Crm_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference/reference_markers.hmm GCF_000330705.1_Crm_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:38,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:38,907] [INFO] Found 6/6 markers.
[2024-01-24 13:25:38,932] [INFO] Query marker FASTA was written to GCF_000330705.1_Crm_genomic.fna/markers.fasta
[2024-01-24 13:25:38,932] [INFO] Task started: Blastn
[2024-01-24 13:25:38,932] [INFO] Running command: blastn -query GCF_000330705.1_Crm_genomic.fna/markers.fasta -db /var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference/reference_markers.fasta -out GCF_000330705.1_Crm_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:39,507] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:39,510] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:39,510] [INFO] Target genome list was writen to GCF_000330705.1_Crm_genomic.fna/target_genomes.txt
[2024-01-24 13:25:39,521] [INFO] Task started: fastANI
[2024-01-24 13:25:39,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cbb86fd-bf2d-4d6a-b279-35d349522654/GCF_000330705.1_Crm_genomic.fna.gz --refList GCF_000330705.1_Crm_genomic.fna/target_genomes.txt --output GCF_000330705.1_Crm_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:47,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:47,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:47,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:47,417] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:47,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:47,417] [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 carnicancri	strain=Crm	GCA_000330705.1	558170	558170	type	True	100.0	884	884	95	conclusive
Salinicoccus sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	93.1785	753	884	95	below_threshold
Salinicoccus halodurans	strain=CGMCC 1.6501	GCA_900114445.1	407035	407035	type	True	81.622	568	884	95	below_threshold
Salinicoccus luteus	strain=DSM 17002	GCA_000712035.1	367840	367840	type	True	78.5515	244	884	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	78.1338	213	884	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	78.0067	232	884	95	below_threshold
Salinicoccus albus	strain=YIM-Y21	GCA_000385175.1	418756	418756	type	True	77.8664	221	884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:47,419] [INFO] DFAST Taxonomy check result was written to GCF_000330705.1_Crm_genomic.fna/tc_result.tsv
[2024-01-24 13:25:47,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:47,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:47,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference/checkm_data
[2024-01-24 13:25:47,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:47,452] [INFO] Task started: CheckM
[2024-01-24 13:25:47,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000330705.1_Crm_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000330705.1_Crm_genomic.fna/checkm_input GCF_000330705.1_Crm_genomic.fna/checkm_result
[2024-01-24 13:26:15,726] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:15,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:15,747] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:15,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:15,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000330705.1_Crm_genomic.fna/markers.fasta)
[2024-01-24 13:26:15,748] [INFO] Task started: Blastn
[2024-01-24 13:26:15,748] [INFO] Running command: blastn -query GCF_000330705.1_Crm_genomic.fna/markers.fasta -db /var/lib/cwl/stg9761a6c5-7658-424f-885c-6f3564d7d69a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000330705.1_Crm_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:16,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:16,597] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:16,598] [INFO] Target genome list was writen to GCF_000330705.1_Crm_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:16,612] [INFO] Task started: fastANI
[2024-01-24 13:26:16,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cbb86fd-bf2d-4d6a-b279-35d349522654/GCF_000330705.1_Crm_genomic.fna.gz --refList GCF_000330705.1_Crm_genomic.fna/target_genomes_gtdb.txt --output GCF_000330705.1_Crm_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:21,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:21,046] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:21,047] [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_000330705.1	s__Salinicoccus carnicancri	100.0	883	884	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_000986795.1	s__Salinicoccus sediminis	93.1785	753	884	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113295.1	s__Salinicoccus stercoripullorum	88.2839	657	884	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114445.1	s__Salinicoccus halodurans	81.6346	567	884	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000712035.1	s__Salinicoccus luteus	78.5515	244	884	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	78.1357	214	884	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	77.9913	233	884	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385175.1	s__Salinicoccus albus	77.8636	220	884	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 13:26:21,048] [INFO] GTDB search result was written to GCF_000330705.1_Crm_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:21,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:21,051] [INFO] DFAST_QC result json was written to GCF_000330705.1_Crm_genomic.fna/dqc_result.json
[2024-01-24 13:26:21,051] [INFO] DFAST_QC completed!
[2024-01-24 13:26:21,052] [INFO] Total running time: 0h0m51s