[2024-01-24 13:55:27,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:27,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:27,282] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference
[2024-01-24 13:55:28,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:28,456] [INFO] Task started: Prodigal
[2024-01-24 13:55:28,457] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d596ca5-2a44-4b51-95b7-d6ed0cc80244/GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna.gz | prodigal -d GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/cds.fna -a GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,410] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,411] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,411] [INFO] Running command: hmmsearch --tblout GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference/reference_markers.hmm GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:32,595] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:32,596] [INFO] Found 6/6 markers.
[2024-01-24 13:55:32,615] [INFO] Query marker FASTA was written to GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/markers.fasta
[2024-01-24 13:55:32,615] [INFO] Task started: Blastn
[2024-01-24 13:55:32,616] [INFO] Running command: blastn -query GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference/reference_markers.fasta -out GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:33,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:33,174] [INFO] Selected 10 target genomes.
[2024-01-24 13:55:33,174] [INFO] Target genome list was writen to GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/target_genomes.txt
[2024-01-24 13:55:33,199] [INFO] Task started: fastANI
[2024-01-24 13:55:33,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d596ca5-2a44-4b51-95b7-d6ed0cc80244/GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna.gz --refList GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/target_genomes.txt --output GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:37,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:37,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:37,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:37,469] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:37,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:37,469] [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
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	100.0	751	752	95	conclusive
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.9749	348	752	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.9309	352	752	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.1043	197	752	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.0756	182	752	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	77.9749	237	752	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.8633	185	752	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.2686	149	752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:37,471] [INFO] DFAST Taxonomy check result was written to GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/tc_result.tsv
[2024-01-24 13:55:37,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:37,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:37,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference/checkm_data
[2024-01-24 13:55:37,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:37,496] [INFO] Task started: CheckM
[2024-01-24 13:55:37,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/checkm_input GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/checkm_result
[2024-01-24 13:55:56,031] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:56,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:56,050] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:56,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:56,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/markers.fasta)
[2024-01-24 13:55:56,051] [INFO] Task started: Blastn
[2024-01-24 13:55:56,051] [INFO] Running command: blastn -query GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2efd7a4-f9ac-4112-865a-c6889d36ebf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:56,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:56,816] [INFO] Selected 13 target genomes.
[2024-01-24 13:55:56,816] [INFO] Target genome list was writen to GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:56,829] [INFO] Task started: fastANI
[2024-01-24 13:55:56,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d596ca5-2a44-4b51-95b7-d6ed0cc80244/GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna.gz --refList GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/target_genomes_gtdb.txt --output GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:02,465] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:02,476] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:02,476] [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_000445475.1	s__Sulfurimonas hongkongensis	100.0	751	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000242915.1	s__Sulfurimonas gotlandica	78.988	347	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016744025.1	s__Sulfurimonas sp016744025	78.7115	288	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732645.1	s__Sulfurimonas sp002732645	78.7107	214	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153755.1	s__Sulfurimonas sp013153755	78.4251	206	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016735225.1	s__Sulfurimonas sp016735225	78.1883	196	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012965.1	s__Sulfurimonas denitrificans	77.9749	237	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357825.1	s__Sulfurimonas sp017357825	77.9365	147	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487435.1	s__Sulfurimonas sp015487435	77.7037	151	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822665.1	s__Sulfurimonas sp018822665	77.5362	144	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCA_001829785.1	s__Sulfurimonas sp001829785	77.4443	200	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
GCF_009192995.1	s__Sulfurimonas indica	77.3637	146	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733945.2	s__Sulfurimonas sp002733945	77.2922	149	752	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:02,478] [INFO] GTDB search result was written to GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:02,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:02,481] [INFO] DFAST_QC result json was written to GCF_000445475.1_Version_1_of_the_Sulfurimonas_hongkongensis_AST-10_genome_genomic.fna/dqc_result.json
[2024-01-24 13:56:02,481] [INFO] DFAST_QC completed!
[2024-01-24 13:56:02,481] [INFO] Total running time: 0h0m35s