[2023-06-30 14:47:59,805] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:47:59,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:47:59,809] [INFO] DQC Reference Directory: /var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference
[2023-06-30 14:48:01,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:48:01,172] [INFO] Task started: Prodigal
[2023-06-30 14:48:01,172] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcefc0f8-1d17-45e3-85ad-f976e38d1de2/GCA_016744905.1_ASM1674490v1_genomic.fna.gz | prodigal -d GCA_016744905.1_ASM1674490v1_genomic.fna/cds.fna -a GCA_016744905.1_ASM1674490v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:48:06,980] [INFO] Task succeeded: Prodigal
[2023-06-30 14:48:06,981] [INFO] Task started: HMMsearch
[2023-06-30 14:48:06,981] [INFO] Running command: hmmsearch --tblout GCA_016744905.1_ASM1674490v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference/reference_markers.hmm GCA_016744905.1_ASM1674490v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:48:07,253] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:48:07,254] [INFO] Found 6/6 markers.
[2023-06-30 14:48:07,287] [INFO] Query marker FASTA was written to GCA_016744905.1_ASM1674490v1_genomic.fna/markers.fasta
[2023-06-30 14:48:07,287] [INFO] Task started: Blastn
[2023-06-30 14:48:07,287] [INFO] Running command: blastn -query GCA_016744905.1_ASM1674490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference/reference_markers.fasta -out GCA_016744905.1_ASM1674490v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:07,881] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:07,885] [INFO] Selected 30 target genomes.
[2023-06-30 14:48:07,885] [INFO] Target genome list was writen to GCA_016744905.1_ASM1674490v1_genomic.fna/target_genomes.txt
[2023-06-30 14:48:07,893] [INFO] Task started: fastANI
[2023-06-30 14:48:07,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcefc0f8-1d17-45e3-85ad-f976e38d1de2/GCA_016744905.1_ASM1674490v1_genomic.fna.gz --refList GCA_016744905.1_ASM1674490v1_genomic.fna/target_genomes.txt --output GCA_016744905.1_ASM1674490v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:48:19,972] [INFO] Task succeeded: fastANI
[2023-06-30 14:48:19,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:48:19,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:48:19,983] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:48:19,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:48:19,983] [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
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.6664	94	942	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.5239	79	942	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.4301	106	942	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.2577	113	942	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.2389	113	942	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.1639	77	942	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	77.1537	72	942	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	76.8692	60	942	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:48:19,993] [INFO] DFAST Taxonomy check result was written to GCA_016744905.1_ASM1674490v1_genomic.fna/tc_result.tsv
[2023-06-30 14:48:19,994] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:48:19,994] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:48:19,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference/checkm_data
[2023-06-30 14:48:19,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:48:20,037] [INFO] Task started: CheckM
[2023-06-30 14:48:20,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016744905.1_ASM1674490v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016744905.1_ASM1674490v1_genomic.fna/checkm_input GCA_016744905.1_ASM1674490v1_genomic.fna/checkm_result
[2023-06-30 14:48:44,559] [INFO] Task succeeded: CheckM
[2023-06-30 14:48:44,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:48:44,580] [INFO] ===== Completeness check finished =====
[2023-06-30 14:48:44,581] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:48:44,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016744905.1_ASM1674490v1_genomic.fna/markers.fasta)
[2023-06-30 14:48:44,582] [INFO] Task started: Blastn
[2023-06-30 14:48:44,582] [INFO] Running command: blastn -query GCA_016744905.1_ASM1674490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga039d8c8-e41d-487e-89f0-091cd8fc4e09/dqc_reference/reference_markers_gtdb.fasta -out GCA_016744905.1_ASM1674490v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:45,411] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:45,415] [INFO] Selected 22 target genomes.
[2023-06-30 14:48:45,415] [INFO] Target genome list was writen to GCA_016744905.1_ASM1674490v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:48:45,425] [INFO] Task started: fastANI
[2023-06-30 14:48:45,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcefc0f8-1d17-45e3-85ad-f976e38d1de2/GCA_016744905.1_ASM1674490v1_genomic.fna.gz --refList GCA_016744905.1_ASM1674490v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016744905.1_ASM1674490v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:48:54,246] [INFO] Task succeeded: fastANI
[2023-06-30 14:48:54,269] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:48:54,270] [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
GCA_016744905.1	s__BB10 sp016744905	100.0	932	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__BB10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014381585.1	s__Sulfurimonas ponti	77.9988	69	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_002335055.1	s__Sulfurimonas sp002335055	77.8608	86	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	-
GCF_017357825.1	s__Sulfurimonas sp017357825	77.7726	87	942	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	77.6912	68	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265475.1	s__Sulfurimonas marisnigri	77.6289	96	942	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	77.5239	79	942	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	77.493	100	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018698455.1	s__Sulfurimonas sp018698455	77.3296	100	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493495.1	s__S145-25 sp015493495	77.2917	71	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__S145-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138865.1	s__GLR69 sp013138865	77.2829	106	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__GLR69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781365.1	s__Sulfurimonas sp002781365	77.1675	93	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.89	0.98	0.96	19	-
GCA_018825665.1	s__Sulfurimonas sp018825665	77.1648	67	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	0.97	0.97	2	-
GCA_016744115.1	s__Sulfurimonas sp016744115	76.9306	79	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733155.1	s__Sulfurimonas sp002733155	76.8018	83	942	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	76.7656	58	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCA_015487265.1	s__Sulfurimonas sp015487265	76.7558	84	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978465.1	s__Sulfurimonas sp003978465	76.712	70	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963655.1	s__GCA-2733885 sp012963655	76.668	63	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__GCA-2733885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938175.1	s__Sulfurimonas sp016938175	76.4419	73	942	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:48:54,272] [INFO] GTDB search result was written to GCA_016744905.1_ASM1674490v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:48:54,272] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:48:54,278] [INFO] DFAST_QC result json was written to GCA_016744905.1_ASM1674490v1_genomic.fna/dqc_result.json
[2023-06-30 14:48:54,278] [INFO] DFAST_QC completed!
[2023-06-30 14:48:54,278] [INFO] Total running time: 0h0m54s