[2024-01-24 13:28:11,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference
[2024-01-24 13:28:12,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:12,970] [INFO] Task started: Prodigal
[2024-01-24 13:28:12,970] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d3f62aa-2881-4adf-b312-764726d92f69/GCF_009258045.1_ASM925804v1_genomic.fna.gz | prodigal -d GCF_009258045.1_ASM925804v1_genomic.fna/cds.fna -a GCF_009258045.1_ASM925804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:16,825] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:16,826] [INFO] Task started: HMMsearch
[2024-01-24 13:28:16,826] [INFO] Running command: hmmsearch --tblout GCF_009258045.1_ASM925804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference/reference_markers.hmm GCF_009258045.1_ASM925804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:17,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:17,051] [INFO] Found 6/6 markers.
[2024-01-24 13:28:17,078] [INFO] Query marker FASTA was written to GCF_009258045.1_ASM925804v1_genomic.fna/markers.fasta
[2024-01-24 13:28:17,078] [INFO] Task started: Blastn
[2024-01-24 13:28:17,078] [INFO] Running command: blastn -query GCF_009258045.1_ASM925804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference/reference_markers.fasta -out GCF_009258045.1_ASM925804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:17,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:17,680] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:17,680] [INFO] Target genome list was writen to GCF_009258045.1_ASM925804v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:17,783] [INFO] Task started: fastANI
[2024-01-24 13:28:17,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d3f62aa-2881-4adf-b312-764726d92f69/GCF_009258045.1_ASM925804v1_genomic.fna.gz --refList GCF_009258045.1_ASM925804v1_genomic.fna/target_genomes.txt --output GCF_009258045.1_ASM925804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:22,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:22,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:22,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:22,333] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:22,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:22,334] [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 xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	100.0	638	638	95	conclusive
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	80.7309	366	638	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	79.1073	303	638	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.7732	235	638	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.7655	237	638	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.7499	197	638	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.5499	200	638	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	78.2037	118	638	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.8087	177	638	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.8045	159	638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:22,336] [INFO] DFAST Taxonomy check result was written to GCF_009258045.1_ASM925804v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:22,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:22,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:22,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference/checkm_data
[2024-01-24 13:28:22,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:22,366] [INFO] Task started: CheckM
[2024-01-24 13:28:22,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009258045.1_ASM925804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009258045.1_ASM925804v1_genomic.fna/checkm_input GCF_009258045.1_ASM925804v1_genomic.fna/checkm_result
[2024-01-24 13:28:41,210] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:41,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,234] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:41,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:41,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009258045.1_ASM925804v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:41,235] [INFO] Task started: Blastn
[2024-01-24 13:28:41,235] [INFO] Running command: blastn -query GCF_009258045.1_ASM925804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfb40982-d976-4678-84c3-74e1fec70645/dqc_reference/reference_markers_gtdb.fasta -out GCF_009258045.1_ASM925804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,114] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:42,114] [INFO] Target genome list was writen to GCF_009258045.1_ASM925804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:42,213] [INFO] Task started: fastANI
[2024-01-24 13:28:42,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d3f62aa-2881-4adf-b312-764726d92f69/GCF_009258045.1_ASM925804v1_genomic.fna.gz --refList GCF_009258045.1_ASM925804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009258045.1_ASM925804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:46,965] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:46,979] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:46,980] [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_009883775.1	s__Sulfurimonas sp002452895	98.6196	583	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	conclusive
GCA_002899765.1	s__Sulfurimonas sp002899765	81.7553	376	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859695.1	s__Sulfurimonas sp014859695	81.1977	346	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217605.1	s__Sulfurimonas crateris	80.7309	366	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903705.1	s__Sulfurimonas sp903903705	79.8602	184	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829675.1	s__Sulfurimonas sp001829675	79.6503	320	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.77	99.75	0.96	0.96	4	-
GCA_001829785.1	s__Sulfurimonas sp001829785	79.5408	346	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
GCA_001829715.1	s__Sulfurimonas sp001829715	79.4533	338	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCF_000012965.1	s__Sulfurimonas denitrificans	79.0925	304	638	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445475.1	s__Sulfurimonas hongkongensis	77.8283	176	638	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 13:28:46,981] [INFO] GTDB search result was written to GCF_009258045.1_ASM925804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:46,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:46,985] [INFO] DFAST_QC result json was written to GCF_009258045.1_ASM925804v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:46,985] [INFO] DFAST_QC completed!
[2024-01-24 13:28:46,985] [INFO] Total running time: 0h0m35s