[2024-01-24 12:44:11,081] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,084] [INFO] DQC Reference Directory: /var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference
[2024-01-24 12:44:12,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,469] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg619be9d7-5ca8-49b5-a760-1610d7f5100b/GCF_014634945.1_ASM1463494v1_genomic.fna.gz | prodigal -d GCF_014634945.1_ASM1463494v1_genomic.fna/cds.fna -a GCF_014634945.1_ASM1463494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:19,832] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:19,833] [INFO] Task started: HMMsearch
[2024-01-24 12:44:19,833] [INFO] Running command: hmmsearch --tblout GCF_014634945.1_ASM1463494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference/reference_markers.hmm GCF_014634945.1_ASM1463494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:20,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:20,142] [INFO] Found 6/6 markers.
[2024-01-24 12:44:20,169] [INFO] Query marker FASTA was written to GCF_014634945.1_ASM1463494v1_genomic.fna/markers.fasta
[2024-01-24 12:44:20,169] [INFO] Task started: Blastn
[2024-01-24 12:44:20,170] [INFO] Running command: blastn -query GCF_014634945.1_ASM1463494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference/reference_markers.fasta -out GCF_014634945.1_ASM1463494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:20,791] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:20,794] [INFO] Selected 11 target genomes.
[2024-01-24 12:44:20,795] [INFO] Target genome list was writen to GCF_014634945.1_ASM1463494v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:20,805] [INFO] Task started: fastANI
[2024-01-24 12:44:20,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg619be9d7-5ca8-49b5-a760-1610d7f5100b/GCF_014634945.1_ASM1463494v1_genomic.fna.gz --refList GCF_014634945.1_ASM1463494v1_genomic.fna/target_genomes.txt --output GCF_014634945.1_ASM1463494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:27,228] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:27,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:27,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:27,236] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:27,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:27,237] [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 roseus	strain=CCM 3516	GCA_014634945.1	45670	45670	type	True	100.0	826	826	95	conclusive
Salinicoccus roseus	strain=DSM 5351	GCA_003814515.1	45670	45670	type	True	99.9878	826	826	95	conclusive
Salinicoccus luteus	strain=DSM 17002	GCA_000712035.1	367840	367840	type	True	89.0528	713	826	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	80.4214	468	826	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	80.1672	427	826	95	below_threshold
Salinicoccus sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	78.9055	275	826	95	below_threshold
Salinicoccus alkaliphilus	strain=DSM 16010	GCA_900142805.1	148453	148453	type	True	77.6441	139	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:27,238] [INFO] DFAST Taxonomy check result was written to GCF_014634945.1_ASM1463494v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:27,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:27,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:27,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference/checkm_data
[2024-01-24 12:44:27,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:27,271] [INFO] Task started: CheckM
[2024-01-24 12:44:27,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014634945.1_ASM1463494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014634945.1_ASM1463494v1_genomic.fna/checkm_input GCF_014634945.1_ASM1463494v1_genomic.fna/checkm_result
[2024-01-24 12:44:55,873] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:55,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:55,895] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:55,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:55,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014634945.1_ASM1463494v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:55,897] [INFO] Task started: Blastn
[2024-01-24 12:44:55,897] [INFO] Running command: blastn -query GCF_014634945.1_ASM1463494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga27fd3c2-cd03-4da8-a956-4ba0b795a7b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014634945.1_ASM1463494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:56,736] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:56,749] [INFO] Selected 11 target genomes.
[2024-01-24 12:44:56,750] [INFO] Target genome list was writen to GCF_014634945.1_ASM1463494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:56,765] [INFO] Task started: fastANI
[2024-01-24 12:44:56,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg619be9d7-5ca8-49b5-a760-1610d7f5100b/GCF_014634945.1_ASM1463494v1_genomic.fna.gz --refList GCF_014634945.1_ASM1463494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014634945.1_ASM1463494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:03,762] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:03,769] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:03,769] [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_003814515.1	s__Salinicoccus roseus	99.9878	826	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	97.90	96.75	0.92	0.87	5	conclusive
GCF_000712035.1	s__Salinicoccus luteus	89.0728	713	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_007713705.1	s__Salinicoccus cyprini	80.4214	468	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	80.1672	427	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_000986795.1	s__Salinicoccus sediminis	78.9055	275	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_019113295.1	s__Salinicoccus stercoripullorum	77.889	234	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_900142805.1	s__Salinicoccus alkaliphilus	77.6386	140	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 12:45:03,771] [INFO] GTDB search result was written to GCF_014634945.1_ASM1463494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:03,772] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:03,775] [INFO] DFAST_QC result json was written to GCF_014634945.1_ASM1463494v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:03,775] [INFO] DFAST_QC completed!
[2024-01-24 12:45:03,775] [INFO] Total running time: 0h0m53s