[2023-06-30 21:18:03,656] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:18:03,663] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:18:03,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference
[2023-06-30 21:18:06,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:18:06,689] [INFO] Task started: Prodigal
[2023-06-30 21:18:06,690] [INFO] Running command: gunzip -c /var/lib/cwl/stga6eccb7a-e0fe-4754-b25b-b01707f1f824/GCA_015658735.1_ASM1565873v1_genomic.fna.gz | prodigal -d GCA_015658735.1_ASM1565873v1_genomic.fna/cds.fna -a GCA_015658735.1_ASM1565873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:18:09,624] [INFO] Task succeeded: Prodigal
[2023-06-30 21:18:09,625] [INFO] Task started: HMMsearch
[2023-06-30 21:18:09,625] [INFO] Running command: hmmsearch --tblout GCA_015658735.1_ASM1565873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference/reference_markers.hmm GCA_015658735.1_ASM1565873v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:18:09,851] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:18:09,853] [INFO] Found 6/6 markers.
[2023-06-30 21:18:09,896] [INFO] Query marker FASTA was written to GCA_015658735.1_ASM1565873v1_genomic.fna/markers.fasta
[2023-06-30 21:18:09,897] [INFO] Task started: Blastn
[2023-06-30 21:18:09,897] [INFO] Running command: blastn -query GCA_015658735.1_ASM1565873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference/reference_markers.fasta -out GCA_015658735.1_ASM1565873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:18:10,684] [INFO] Task succeeded: Blastn
[2023-06-30 21:18:10,689] [INFO] Selected 10 target genomes.
[2023-06-30 21:18:10,689] [INFO] Target genome list was writen to GCA_015658735.1_ASM1565873v1_genomic.fna/target_genomes.txt
[2023-06-30 21:18:10,691] [INFO] Task started: fastANI
[2023-06-30 21:18:10,691] [INFO] Running command: fastANI --query /var/lib/cwl/stga6eccb7a-e0fe-4754-b25b-b01707f1f824/GCA_015658735.1_ASM1565873v1_genomic.fna.gz --refList GCA_015658735.1_ASM1565873v1_genomic.fna/target_genomes.txt --output GCA_015658735.1_ASM1565873v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:18:14,371] [INFO] Task succeeded: fastANI
[2023-06-30 21:18:14,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:18:14,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:18:14,382] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:18:14,382] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:18:14,382] [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 paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	78.2901	109	540	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.2611	199	540	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.1456	191	540	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.1331	173	540	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.0869	167	540	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.9181	150	540	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.893	156	540	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	77.6396	117	540	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	77.3837	112	540	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.2735	136	540	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:18:14,384] [INFO] DFAST Taxonomy check result was written to GCA_015658735.1_ASM1565873v1_genomic.fna/tc_result.tsv
[2023-06-30 21:18:14,385] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:18:14,385] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:18:14,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference/checkm_data
[2023-06-30 21:18:14,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:18:14,406] [INFO] Task started: CheckM
[2023-06-30 21:18:14,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015658735.1_ASM1565873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015658735.1_ASM1565873v1_genomic.fna/checkm_input GCA_015658735.1_ASM1565873v1_genomic.fna/checkm_result
[2023-06-30 21:18:33,241] [INFO] Task succeeded: CheckM
[2023-06-30 21:18:33,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:18:33,260] [INFO] ===== Completeness check finished =====
[2023-06-30 21:18:33,261] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:18:33,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015658735.1_ASM1565873v1_genomic.fna/markers.fasta)
[2023-06-30 21:18:33,262] [INFO] Task started: Blastn
[2023-06-30 21:18:33,262] [INFO] Running command: blastn -query GCA_015658735.1_ASM1565873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc4304ef-a224-40ef-83ba-052f8d326bb8/dqc_reference/reference_markers_gtdb.fasta -out GCA_015658735.1_ASM1565873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:18:34,079] [INFO] Task succeeded: Blastn
[2023-06-30 21:18:34,083] [INFO] Selected 11 target genomes.
[2023-06-30 21:18:34,083] [INFO] Target genome list was writen to GCA_015658735.1_ASM1565873v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:18:34,087] [INFO] Task started: fastANI
[2023-06-30 21:18:34,087] [INFO] Running command: fastANI --query /var/lib/cwl/stga6eccb7a-e0fe-4754-b25b-b01707f1f824/GCA_015658735.1_ASM1565873v1_genomic.fna.gz --refList GCA_015658735.1_ASM1565873v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015658735.1_ASM1565873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:18:38,597] [INFO] Task succeeded: fastANI
[2023-06-30 21:18:38,612] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:18:38,612] [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_002335055.1	s__Sulfurimonas sp002335055	99.9679	501	540	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	conclusive
GCA_003978465.1	s__Sulfurimonas sp003978465	89.9605	391	540	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	88.2579	460	540	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663215.1	s__Sulfurimonas sp015663215	83.3455	268	540	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	80.3855	239	540	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488615.1	s__Sulfurimonas sp015488615	79.7709	240	540	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCF_017357825.1	s__Sulfurimonas sp017357825	79.4978	239	540	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	78.5562	121	540	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	78.1224	145	540	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.6688	142	540	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 21:18:38,615] [INFO] GTDB search result was written to GCA_015658735.1_ASM1565873v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:18:38,616] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:18:38,620] [INFO] DFAST_QC result json was written to GCA_015658735.1_ASM1565873v1_genomic.fna/dqc_result.json
[2023-06-30 21:18:38,620] [INFO] DFAST_QC completed!
[2023-06-30 21:18:38,621] [INFO] Total running time: 0h0m35s