[2024-01-24 12:31:03,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference
[2024-01-24 12:31:04,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,938] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,939] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc6b90bb-a430-4af7-8f31-992a66afadbd/GCF_000597725.1_ASM59772v1_genomic.fna.gz | prodigal -d GCF_000597725.1_ASM59772v1_genomic.fna/cds.fna -a GCF_000597725.1_ASM59772v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:09,431] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:09,431] [INFO] Task started: HMMsearch
[2024-01-24 12:31:09,432] [INFO] Running command: hmmsearch --tblout GCF_000597725.1_ASM59772v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference/reference_markers.hmm GCF_000597725.1_ASM59772v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:09,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:09,677] [INFO] Found 6/6 markers.
[2024-01-24 12:31:09,706] [INFO] Query marker FASTA was written to GCF_000597725.1_ASM59772v1_genomic.fna/markers.fasta
[2024-01-24 12:31:09,707] [INFO] Task started: Blastn
[2024-01-24 12:31:09,707] [INFO] Running command: blastn -query GCF_000597725.1_ASM59772v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference/reference_markers.fasta -out GCF_000597725.1_ASM59772v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:10,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:10,315] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:10,316] [INFO] Target genome list was writen to GCF_000597725.1_ASM59772v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:10,329] [INFO] Task started: fastANI
[2024-01-24 12:31:10,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc6b90bb-a430-4af7-8f31-992a66afadbd/GCF_000597725.1_ASM59772v1_genomic.fna.gz --refList GCF_000597725.1_ASM59772v1_genomic.fna/target_genomes.txt --output GCF_000597725.1_ASM59772v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:17,330] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:17,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:17,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:17,351] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:17,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:17,351] [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
Sulfurospirillum arcachonense	strain=DSM 9755	GCA_000597725.1	57666	57666	type	True	100.0	864	865	95	conclusive
Sulfurospirillum multivorans	strain=DSM 12446	GCA_000568815.1	66821	66821	type	True	77.3483	58	865	95	below_threshold
Sulfurospirillum deleyianum	strain=DSM 6946	GCA_000024885.1	65553	65553	type	True	77.0432	71	865	95	below_threshold
Sulfurospirillum barnesii	strain=SES-3	GCA_000265295.1	44674	44674	type	True	76.5736	82	865	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	76.5625	51	865	95	below_threshold
Campylobacter ornithocola	strain=LMG 29815	GCA_013201605.1	1848766	1848766	type	True	76.3745	54	865	95	below_threshold
Campylobacter coli	strain=LMG 9860	GCA_000254135.2	195	195	type	True	76.2541	50	865	95	below_threshold
Campylobacter armoricus	strain=CCUG 73571	GCA_013372105.1	2505970	2505970	type	True	76.0859	62	865	95	below_threshold
Campylobacter armoricus	strain=CA656	GCA_006176165.1	2505970	2505970	type	True	76.0509	58	865	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	76.029	106	865	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=type strain: CCUG11284	GCA_905410075.1	32022	197	type	True	75.8419	59	865	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	75.8401	59	865	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	75.8238	58	865	95	below_threshold
Campylobacter novaezeelandiae	strain=B423b	GCA_004323845.1	2267891	2267891	type	True	75.8094	56	865	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	75.8024	157	865	95	below_threshold
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	75.7578	61	865	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	75.7304	152	865	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	75.5296	91	865	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	75.4215	91	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:17,355] [INFO] DFAST Taxonomy check result was written to GCF_000597725.1_ASM59772v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:17,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:17,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:17,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference/checkm_data
[2024-01-24 12:31:17,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:17,388] [INFO] Task started: CheckM
[2024-01-24 12:31:17,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000597725.1_ASM59772v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000597725.1_ASM59772v1_genomic.fna/checkm_input GCF_000597725.1_ASM59772v1_genomic.fna/checkm_result
[2024-01-24 12:31:38,766] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:38,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:38,792] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:38,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:38,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000597725.1_ASM59772v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:38,793] [INFO] Task started: Blastn
[2024-01-24 12:31:38,794] [INFO] Running command: blastn -query GCF_000597725.1_ASM59772v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9294f06-ba89-401a-b9bf-fabb34fe9594/dqc_reference/reference_markers_gtdb.fasta -out GCF_000597725.1_ASM59772v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:39,625] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:39,629] [INFO] Selected 9 target genomes.
[2024-01-24 12:31:39,629] [INFO] Target genome list was writen to GCF_000597725.1_ASM59772v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:39,655] [INFO] Task started: fastANI
[2024-01-24 12:31:39,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc6b90bb-a430-4af7-8f31-992a66afadbd/GCF_000597725.1_ASM59772v1_genomic.fna.gz --refList GCF_000597725.1_ASM59772v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000597725.1_ASM59772v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:43,926] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:43,941] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:43,941] [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_000597725.1	s__Sulfurospirillum_A arcachonense	100.0	864	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016744795.1	s__Sulfurospirillum_A sp016744795	79.985	436	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	99.54	99.54	0.95	0.95	2	-
GCA_015662785.1	s__Sulfurospirillum_A arcachonense_A	79.6061	313	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	99.43	99.43	0.82	0.82	2	-
GCA_016735235.1	s__Sulfurospirillum_A sp016735235	78.3125	193	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	99.48	99.48	0.88	0.88	2	-
GCA_002742765.1	s__Sulfurospirillum_A sp002742765	77.6678	247	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	96.93	96.87	0.77	0.74	3	-
GCA_002469305.1	s__Sulfurospirillum_A sp002469305	77.6032	246	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930915.1	s__Sulfurospirillum sp016930915	76.1801	83	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	99.92	99.92	0.95	0.95	2	-
GCA_015488775.1	s__WFNF01 sp015488775	75.7844	69	865	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__WFNF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:43,943] [INFO] GTDB search result was written to GCF_000597725.1_ASM59772v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:43,944] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:43,947] [INFO] DFAST_QC result json was written to GCF_000597725.1_ASM59772v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:43,947] [INFO] DFAST_QC completed!
[2024-01-24 12:31:43,947] [INFO] Total running time: 0h0m40s