[2024-01-24 15:26:55,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference
[2024-01-24 15:26:56,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,434] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,435] [INFO] Running command: gunzip -c /var/lib/cwl/stg69b99706-8729-435c-ad77-3bc2c5c2913c/GCF_007713705.1_ASM771370v1_genomic.fna.gz | prodigal -d GCF_007713705.1_ASM771370v1_genomic.fna/cds.fna -a GCF_007713705.1_ASM771370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:03,860] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:03,860] [INFO] Task started: HMMsearch
[2024-01-24 15:27:03,861] [INFO] Running command: hmmsearch --tblout GCF_007713705.1_ASM771370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference/reference_markers.hmm GCF_007713705.1_ASM771370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:04,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:04,133] [INFO] Found 6/6 markers.
[2024-01-24 15:27:04,162] [INFO] Query marker FASTA was written to GCF_007713705.1_ASM771370v1_genomic.fna/markers.fasta
[2024-01-24 15:27:04,162] [INFO] Task started: Blastn
[2024-01-24 15:27:04,162] [INFO] Running command: blastn -query GCF_007713705.1_ASM771370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference/reference_markers.fasta -out GCF_007713705.1_ASM771370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:04,828] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:04,831] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:04,832] [INFO] Target genome list was writen to GCF_007713705.1_ASM771370v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:04,840] [INFO] Task started: fastANI
[2024-01-24 15:27:04,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b99706-8729-435c-ad77-3bc2c5c2913c/GCF_007713705.1_ASM771370v1_genomic.fna.gz --refList GCF_007713705.1_ASM771370v1_genomic.fna/target_genomes.txt --output GCF_007713705.1_ASM771370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:09,643] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:09,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:09,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:09,651] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:09,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:09,652] [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 cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	100.0	811	811	95	conclusive
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	86.6786	697	811	95	below_threshold
Salinicoccus roseus	strain=DSM 5351	GCA_003814515.1	45670	45670	type	True	80.4727	472	811	95	below_threshold
Salinicoccus roseus	strain=CCM 3516	GCA_014634945.1	45670	45670	type	True	80.4454	473	811	95	below_threshold
Salinicoccus luteus	strain=DSM 17002	GCA_000712035.1	367840	367840	type	True	80.3132	479	811	95	below_threshold
Salinicoccus carnicancri	strain=Crm	GCA_000330705.1	558170	558170	type	True	78.1591	227	811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:09,654] [INFO] DFAST Taxonomy check result was written to GCF_007713705.1_ASM771370v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:09,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:09,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:09,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference/checkm_data
[2024-01-24 15:27:09,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:09,686] [INFO] Task started: CheckM
[2024-01-24 15:27:09,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007713705.1_ASM771370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007713705.1_ASM771370v1_genomic.fna/checkm_input GCF_007713705.1_ASM771370v1_genomic.fna/checkm_result
[2024-01-24 15:27:37,266] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:37,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,284] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:37,284] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:37,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007713705.1_ASM771370v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:37,285] [INFO] Task started: Blastn
[2024-01-24 15:27:37,285] [INFO] Running command: blastn -query GCF_007713705.1_ASM771370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07b555ea-590d-4b33-be03-b94bca20a8a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_007713705.1_ASM771370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:38,117] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:38,120] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:38,121] [INFO] Target genome list was writen to GCF_007713705.1_ASM771370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:38,135] [INFO] Task started: fastANI
[2024-01-24 15:27:38,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b99706-8729-435c-ad77-3bc2c5c2913c/GCF_007713705.1_ASM771370v1_genomic.fna.gz --refList GCF_007713705.1_ASM771370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007713705.1_ASM771370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:43,817] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:43,825] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:43,825] [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_007713705.1	s__Salinicoccus cyprini	100.0	811	811	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_009831115.1	s__Salinicoccus hispanicus	86.6786	697	811	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	80.4727	472	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	97.90	96.75	0.92	0.87	5	-
GCF_000712035.1	s__Salinicoccus luteus	80.3132	479	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000986795.1	s__Salinicoccus sediminis	78.4745	258	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000330705.1	s__Salinicoccus carnicancri	78.1615	228	811	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	77.9254	226	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142805.1	s__Salinicoccus alkaliphilus	77.1679	126	811	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 15:27:43,827] [INFO] GTDB search result was written to GCF_007713705.1_ASM771370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:43,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:43,830] [INFO] DFAST_QC result json was written to GCF_007713705.1_ASM771370v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:43,830] [INFO] DFAST_QC completed!
[2024-01-24 15:27:43,830] [INFO] Total running time: 0h0m49s