[2023-06-16 19:18:29,161] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:18:29,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:18:29,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference
[2023-06-16 19:18:30,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:18:30,362] [INFO] Task started: Prodigal
[2023-06-16 19:18:30,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg46934d2b-1adf-41f9-8f58-2f89c925e720/GCA_013607635.1_ASM1360763v1_genomic.fna.gz | prodigal -d GCA_013607635.1_ASM1360763v1_genomic.fna/cds.fna -a GCA_013607635.1_ASM1360763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:18:33,634] [INFO] Task succeeded: Prodigal
[2023-06-16 19:18:33,635] [INFO] Task started: HMMsearch
[2023-06-16 19:18:33,635] [INFO] Running command: hmmsearch --tblout GCA_013607635.1_ASM1360763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference/reference_markers.hmm GCA_013607635.1_ASM1360763v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:18:33,795] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:18:33,796] [INFO] Found 6/6 markers.
[2023-06-16 19:18:33,812] [INFO] Query marker FASTA was written to GCA_013607635.1_ASM1360763v1_genomic.fna/markers.fasta
[2023-06-16 19:18:33,813] [INFO] Task started: Blastn
[2023-06-16 19:18:33,813] [INFO] Running command: blastn -query GCA_013607635.1_ASM1360763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference/reference_markers.fasta -out GCA_013607635.1_ASM1360763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:18:34,372] [INFO] Task succeeded: Blastn
[2023-06-16 19:18:34,376] [INFO] Selected 23 target genomes.
[2023-06-16 19:18:34,376] [INFO] Target genome list was writen to GCA_013607635.1_ASM1360763v1_genomic.fna/target_genomes.txt
[2023-06-16 19:18:34,382] [INFO] Task started: fastANI
[2023-06-16 19:18:34,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg46934d2b-1adf-41f9-8f58-2f89c925e720/GCA_013607635.1_ASM1360763v1_genomic.fna.gz --refList GCA_013607635.1_ASM1360763v1_genomic.fna/target_genomes.txt --output GCA_013607635.1_ASM1360763v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:18:42,895] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:42,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:18:42,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:18:42,908] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:18:42,908] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:18:42,908] [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 indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.6382	140	431	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	77.6332	137	431	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.2384	101	431	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.098	58	431	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	76.8785	104	431	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	76.8333	69	431	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	76.7991	62	431	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	76.7893	56	431	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	76.7323	58	431	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	76.6913	97	431	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	76.6807	69	431	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	76.6769	61	431	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	76.2131	70	431	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:18:42,910] [INFO] DFAST Taxonomy check result was written to GCA_013607635.1_ASM1360763v1_genomic.fna/tc_result.tsv
[2023-06-16 19:18:42,911] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:18:42,911] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:18:42,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference/checkm_data
[2023-06-16 19:18:42,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:18:42,929] [INFO] Task started: CheckM
[2023-06-16 19:18:42,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013607635.1_ASM1360763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013607635.1_ASM1360763v1_genomic.fna/checkm_input GCA_013607635.1_ASM1360763v1_genomic.fna/checkm_result
[2023-06-16 19:19:00,254] [INFO] Task succeeded: CheckM
[2023-06-16 19:19:00,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 3.46%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-16 19:19:00,276] [INFO] ===== Completeness check finished =====
[2023-06-16 19:19:00,276] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:19:00,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013607635.1_ASM1360763v1_genomic.fna/markers.fasta)
[2023-06-16 19:19:00,277] [INFO] Task started: Blastn
[2023-06-16 19:19:00,277] [INFO] Running command: blastn -query GCA_013607635.1_ASM1360763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44db835d-a7ec-4323-a2f4-2aca279d0a2b/dqc_reference/reference_markers_gtdb.fasta -out GCA_013607635.1_ASM1360763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:19:01,038] [INFO] Task succeeded: Blastn
[2023-06-16 19:19:01,041] [INFO] Selected 18 target genomes.
[2023-06-16 19:19:01,042] [INFO] Target genome list was writen to GCA_013607635.1_ASM1360763v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:19:01,082] [INFO] Task started: fastANI
[2023-06-16 19:19:01,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg46934d2b-1adf-41f9-8f58-2f89c925e720/GCA_013607635.1_ASM1360763v1_genomic.fna.gz --refList GCA_013607635.1_ASM1360763v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013607635.1_ASM1360763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:19:08,307] [INFO] Task succeeded: fastANI
[2023-06-16 19:19:08,321] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:19:08,321] [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_013607635.1	s__Sulfurimonas sp013607635	100.0	427	431	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	78.3074	158	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192995.1	s__Sulfurimonas indica	77.6382	140	431	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	77.6332	137	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607665.1	s__Sulfurimonas sp013607665	77.4962	129	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487265.1	s__Sulfurimonas sp015487265	77.493	89	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892995.1	s__CAITKP01 sp903892995	77.1859	64	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.47	98.97	0.95	0.95	3	-
GCA_016937915.1	s__Sulfurimonas sp016937915	76.9901	50	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938175.1	s__Sulfurimonas sp016938175	76.9638	89	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905115.1	s__Sulfurimonas sediminis	76.8785	104	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009258225.1	s__Sulfurimonas sp009258225	76.803	71	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009068765.1	s__Sulfurimonas sp009068765	76.6913	97	431	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	76.6807	69	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452425.1	s__Sulfurimonas sp002452425	76.4867	52	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.33	99.33	0.89	0.89	2	-
GCA_018824305.1	s__CAITKP01 sp018824305	76.4803	67	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017357825.1	s__Sulfurimonas sp017357825	76.3809	75	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488855.1	s__Sulfurimonas sp015488855	76.2354	56	431	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.17	99.17	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:19:08,323] [INFO] GTDB search result was written to GCA_013607635.1_ASM1360763v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:19:08,324] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:19:08,328] [INFO] DFAST_QC result json was written to GCA_013607635.1_ASM1360763v1_genomic.fna/dqc_result.json
[2023-06-16 19:19:08,328] [INFO] DFAST_QC completed!
[2023-06-16 19:19:08,328] [INFO] Total running time: 0h0m39s