[2024-01-24 13:49:33,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference
[2024-01-24 13:49:34,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,640] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f158ee4-8ee6-4aa9-a0dd-1d8f6b9a2d57/GCF_000986795.1_ASM98679v1_genomic.fna.gz | prodigal -d GCF_000986795.1_ASM98679v1_genomic.fna/cds.fna -a GCF_000986795.1_ASM98679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,495] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,496] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,496] [INFO] Running command: hmmsearch --tblout GCF_000986795.1_ASM98679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference/reference_markers.hmm GCF_000986795.1_ASM98679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,780] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,781] [INFO] Found 6/6 markers.
[2024-01-24 13:49:42,825] [INFO] Query marker FASTA was written to GCF_000986795.1_ASM98679v1_genomic.fna/markers.fasta
[2024-01-24 13:49:42,825] [INFO] Task started: Blastn
[2024-01-24 13:49:42,825] [INFO] Running command: blastn -query GCF_000986795.1_ASM98679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference/reference_markers.fasta -out GCF_000986795.1_ASM98679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,479] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:43,480] [INFO] Target genome list was writen to GCF_000986795.1_ASM98679v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,490] [INFO] Task started: fastANI
[2024-01-24 13:49:43,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f158ee4-8ee6-4aa9-a0dd-1d8f6b9a2d57/GCF_000986795.1_ASM98679v1_genomic.fna.gz --refList GCF_000986795.1_ASM98679v1_genomic.fna/target_genomes.txt --output GCF_000986795.1_ASM98679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,095] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:58,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,095] [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 sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	100.0	854	854	95	conclusive
Salinicoccus carnicancri	strain=Crm	GCA_000330705.1	558170	558170	type	True	93.2614	746	854	95	below_threshold
Salinicoccus halodurans	strain=CGMCC 1.6501	GCA_900114445.1	407035	407035	type	True	82.415	617	854	95	below_threshold
Salinicoccus roseus	strain=DSM 5351	GCA_003814515.1	45670	45670	type	True	78.8558	285	854	95	below_threshold
Salinicoccus roseus	strain=CCM 3516	GCA_014634945.1	45670	45670	type	True	78.6662	289	854	95	below_threshold
Salinicoccus albus	strain=YIM-Y21	GCA_000385175.1	418756	418756	type	True	78.5317	229	854	95	below_threshold
Salinicoccus luteus	strain=DSM 17002	GCA_000712035.1	367840	367840	type	True	78.492	271	854	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	78.4516	264	854	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	78.112	218	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,097] [INFO] DFAST Taxonomy check result was written to GCF_000986795.1_ASM98679v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,098] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference/checkm_data
[2024-01-24 13:49:58,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,129] [INFO] Task started: CheckM
[2024-01-24 13:49:58,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000986795.1_ASM98679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000986795.1_ASM98679v1_genomic.fna/checkm_input GCF_000986795.1_ASM98679v1_genomic.fna/checkm_result
[2024-01-24 13:50:28,415] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:28,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,435] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:28,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:28,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000986795.1_ASM98679v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:28,436] [INFO] Task started: Blastn
[2024-01-24 13:50:28,436] [INFO] Running command: blastn -query GCF_000986795.1_ASM98679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45691a91-0b8c-4e31-b248-f366c5977f30/dqc_reference/reference_markers_gtdb.fasta -out GCF_000986795.1_ASM98679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:29,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:29,222] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:29,222] [INFO] Target genome list was writen to GCF_000986795.1_ASM98679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:29,233] [INFO] Task started: fastANI
[2024-01-24 13:50:29,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f158ee4-8ee6-4aa9-a0dd-1d8f6b9a2d57/GCF_000986795.1_ASM98679v1_genomic.fna.gz --refList GCF_000986795.1_ASM98679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000986795.1_ASM98679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:37,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:37,418] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:37,418] [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_000986795.1	s__Salinicoccus sediminis	100.0	854	854	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_000330705.1	s__Salinicoccus carnicancri	93.2614	746	854	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	89.7963	687	854	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	82.415	617	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003814515.1	s__Salinicoccus roseus	78.8558	285	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	97.90	96.75	0.92	0.87	5	-
GCF_000385175.1	s__Salinicoccus albus	78.5433	230	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712035.1	s__Salinicoccus luteus	78.492	271	854	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	78.4499	263	854	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 13:50:37,420] [INFO] GTDB search result was written to GCF_000986795.1_ASM98679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:37,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:37,427] [INFO] DFAST_QC result json was written to GCF_000986795.1_ASM98679v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:37,428] [INFO] DFAST_QC completed!
[2024-01-24 13:50:37,428] [INFO] Total running time: 0h1m4s