[2023-06-16 19:19:44,069] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:19:44,072] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:19:44,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference
[2023-06-16 19:19:45,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:19:45,246] [INFO] Task started: Prodigal
[2023-06-16 19:19:45,247] [INFO] Running command: gunzip -c /var/lib/cwl/stge478255b-fe0c-47e9-a95e-aa0d054027dc/GCA_028698775.1_ASM2869877v1_genomic.fna.gz | prodigal -d GCA_028698775.1_ASM2869877v1_genomic.fna/cds.fna -a GCA_028698775.1_ASM2869877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:19:49,800] [INFO] Task succeeded: Prodigal
[2023-06-16 19:19:49,800] [INFO] Task started: HMMsearch
[2023-06-16 19:19:49,800] [INFO] Running command: hmmsearch --tblout GCA_028698775.1_ASM2869877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference/reference_markers.hmm GCA_028698775.1_ASM2869877v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:19:50,002] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:19:50,003] [INFO] Found 6/6 markers.
[2023-06-16 19:19:50,030] [INFO] Query marker FASTA was written to GCA_028698775.1_ASM2869877v1_genomic.fna/markers.fasta
[2023-06-16 19:19:50,030] [INFO] Task started: Blastn
[2023-06-16 19:19:50,030] [INFO] Running command: blastn -query GCA_028698775.1_ASM2869877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference/reference_markers.fasta -out GCA_028698775.1_ASM2869877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:19:50,627] [INFO] Task succeeded: Blastn
[2023-06-16 19:19:50,631] [INFO] Selected 11 target genomes.
[2023-06-16 19:19:50,632] [INFO] Target genome list was writen to GCA_028698775.1_ASM2869877v1_genomic.fna/target_genomes.txt
[2023-06-16 19:19:50,633] [INFO] Task started: fastANI
[2023-06-16 19:19:50,633] [INFO] Running command: fastANI --query /var/lib/cwl/stge478255b-fe0c-47e9-a95e-aa0d054027dc/GCA_028698775.1_ASM2869877v1_genomic.fna.gz --refList GCA_028698775.1_ASM2869877v1_genomic.fna/target_genomes.txt --output GCA_028698775.1_ASM2869877v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:19:55,347] [INFO] Task succeeded: fastANI
[2023-06-16 19:19:55,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:19:55,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:19:55,357] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:19:55,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:19:55,358] [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	79.3487	341	769	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	79.3452	328	769	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	79.2227	329	769	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.3196	220	769	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.2022	212	769	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.9655	172	769	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.9146	174	769	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	77.0741	119	769	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	76.9888	118	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:19:55,360] [INFO] DFAST Taxonomy check result was written to GCA_028698775.1_ASM2869877v1_genomic.fna/tc_result.tsv
[2023-06-16 19:19:55,361] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:19:55,361] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:19:55,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference/checkm_data
[2023-06-16 19:19:55,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:19:55,389] [INFO] Task started: CheckM
[2023-06-16 19:19:55,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028698775.1_ASM2869877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028698775.1_ASM2869877v1_genomic.fna/checkm_input GCA_028698775.1_ASM2869877v1_genomic.fna/checkm_result
[2023-06-16 19:20:15,376] [INFO] Task succeeded: CheckM
[2023-06-16 19:20:15,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:20:15,394] [INFO] ===== Completeness check finished =====
[2023-06-16 19:20:15,395] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:20:15,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028698775.1_ASM2869877v1_genomic.fna/markers.fasta)
[2023-06-16 19:20:15,395] [INFO] Task started: Blastn
[2023-06-16 19:20:15,395] [INFO] Running command: blastn -query GCA_028698775.1_ASM2869877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde974146-0d87-4d8d-ba3b-62424a2b8b9a/dqc_reference/reference_markers_gtdb.fasta -out GCA_028698775.1_ASM2869877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:20:16,262] [INFO] Task succeeded: Blastn
[2023-06-16 19:20:16,266] [INFO] Selected 9 target genomes.
[2023-06-16 19:20:16,266] [INFO] Target genome list was writen to GCA_028698775.1_ASM2869877v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:20:16,277] [INFO] Task started: fastANI
[2023-06-16 19:20:16,277] [INFO] Running command: fastANI --query /var/lib/cwl/stge478255b-fe0c-47e9-a95e-aa0d054027dc/GCA_028698775.1_ASM2869877v1_genomic.fna.gz --refList GCA_028698775.1_ASM2869877v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028698775.1_ASM2869877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:20:20,698] [INFO] Task succeeded: fastANI
[2023-06-16 19:20:20,707] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:20:20,708] [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_001829715.1	s__Sulfurimonas sp001829715	98.0607	645	769	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	conclusive
GCA_903903705.1	s__Sulfurimonas sp903903705	94.1155	302	769	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	80.9336	405	769	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.77	99.75	0.96	0.96	4	-
GCA_002899765.1	s__Sulfurimonas sp002899765	80.2851	374	769	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829785.1	s__Sulfurimonas sp001829785	79.7736	400	769	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
GCA_014859695.1	s__Sulfurimonas sp014859695	79.5833	337	769	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	79.36	327	769	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	79.2208	330	769	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	79.1992	352	769	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-16 19:20:20,710] [INFO] GTDB search result was written to GCA_028698775.1_ASM2869877v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:20:20,710] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:20:20,714] [INFO] DFAST_QC result json was written to GCA_028698775.1_ASM2869877v1_genomic.fna/dqc_result.json
[2023-06-16 19:20:20,714] [INFO] DFAST_QC completed!
[2023-06-16 19:20:20,714] [INFO] Total running time: 0h0m37s