[2024-01-24 13:01:39,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference
[2024-01-24 13:01:41,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,549] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg42cb7022-478b-4e71-8927-d2655283daa0/GCF_009258225.1_ASM925822v1_genomic.fna.gz | prodigal -d GCF_009258225.1_ASM925822v1_genomic.fna/cds.fna -a GCF_009258225.1_ASM925822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:45,983] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:45,983] [INFO] Task started: HMMsearch
[2024-01-24 13:01:45,983] [INFO] Running command: hmmsearch --tblout GCF_009258225.1_ASM925822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference/reference_markers.hmm GCF_009258225.1_ASM925822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:46,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:46,251] [INFO] Found 6/6 markers.
[2024-01-24 13:01:46,283] [INFO] Query marker FASTA was written to GCF_009258225.1_ASM925822v1_genomic.fna/markers.fasta
[2024-01-24 13:01:46,283] [INFO] Task started: Blastn
[2024-01-24 13:01:46,284] [INFO] Running command: blastn -query GCF_009258225.1_ASM925822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference/reference_markers.fasta -out GCF_009258225.1_ASM925822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:47,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:47,776] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:47,776] [INFO] Target genome list was writen to GCF_009258225.1_ASM925822v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:47,790] [INFO] Task started: fastANI
[2024-01-24 13:01:47,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg42cb7022-478b-4e71-8927-d2655283daa0/GCF_009258225.1_ASM925822v1_genomic.fna.gz --refList GCF_009258225.1_ASM925822v1_genomic.fna/target_genomes.txt --output GCF_009258225.1_ASM925822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:55,574] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:55,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:55,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:55,587] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:55,587] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:55,587] [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 lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	100.0	802	804	95	conclusive
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	78.5758	119	804	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	78.291	162	804	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.2306	184	804	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.1688	195	804	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.156	201	804	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	78.0979	135	804	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.0911	168	804	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.9361	139	804	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.8075	167	804	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.3487	153	804	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	76.5099	72	804	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	76.4915	74	804	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	75.5477	70	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:55,589] [INFO] DFAST Taxonomy check result was written to GCF_009258225.1_ASM925822v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:55,589] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:55,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:55,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference/checkm_data
[2024-01-24 13:01:55,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:55,632] [INFO] Task started: CheckM
[2024-01-24 13:01:55,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009258225.1_ASM925822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009258225.1_ASM925822v1_genomic.fna/checkm_input GCF_009258225.1_ASM925822v1_genomic.fna/checkm_result
[2024-01-24 13:02:18,304] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:18,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:18,350] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:18,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:18,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009258225.1_ASM925822v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:18,351] [INFO] Task started: Blastn
[2024-01-24 13:02:18,351] [INFO] Running command: blastn -query GCF_009258225.1_ASM925822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e786962-e932-47d9-90b3-506ca23ee4b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009258225.1_ASM925822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:19,945] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:19,948] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:19,948] [INFO] Target genome list was writen to GCF_009258225.1_ASM925822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:19,967] [INFO] Task started: fastANI
[2024-01-24 13:02:19,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg42cb7022-478b-4e71-8927-d2655283daa0/GCF_009258225.1_ASM925822v1_genomic.fna.gz --refList GCF_009258225.1_ASM925822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009258225.1_ASM925822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:28,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:28,531] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:28,532] [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_009258225.1	s__Sulfurimonas sp009258225	100.0	801	804	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_014905095.1	s__Sulfurimonas sp014905095	78.8853	163	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905135.1	s__Sulfurimonas paralvinellae	78.5686	121	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242915.1	s__Sulfurimonas gotlandica	78.2441	201	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015265475.1	s__Sulfurimonas marisnigri	78.1908	183	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	78.185	162	804	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	78.0512	181	804	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	77.7642	118	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009883775.1	s__Sulfurimonas sp002452895	77.6115	159	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCA_015488855.1	s__Sulfurimonas sp015488855	77.6078	119	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.17	99.17	0.76	0.76	2	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.5971	146	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764205.1	s__Sulfurimonas sp016764205	77.5761	73	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744025.1	s__Sulfurimonas sp016744025	77.43	191	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829715.1	s__Sulfurimonas sp001829715	77.3682	139	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCF_000445475.1	s__Sulfurimonas hongkongensis	77.3487	153	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381585.1	s__Sulfurimonas ponti	77.2917	140	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_002733155.1	s__Sulfurimonas sp002733155	77.1732	149	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138865.1	s__GLR69 sp013138865	76.4676	87	804	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__GLR69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978465.1	s__Sulfurimonas sp003978465	76.2635	102	804	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 13:02:28,536] [INFO] GTDB search result was written to GCF_009258225.1_ASM925822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:28,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:28,543] [INFO] DFAST_QC result json was written to GCF_009258225.1_ASM925822v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:28,544] [INFO] DFAST_QC completed!
[2024-01-24 13:02:28,544] [INFO] Total running time: 0h0m49s