[2024-01-24 11:04:03,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:04:03,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:04:03,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference
[2024-01-24 11:04:04,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:04:04,511] [INFO] Task started: Prodigal
[2024-01-24 11:04:04,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg034430a1-b914-4d9f-9462-5dea8ad5533f/GCF_016772315.1_ASM1677231v1_genomic.fna.gz | prodigal -d GCF_016772315.1_ASM1677231v1_genomic.fna/cds.fna -a GCF_016772315.1_ASM1677231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:04:19,131] [INFO] Task succeeded: Prodigal
[2024-01-24 11:04:19,132] [INFO] Task started: HMMsearch
[2024-01-24 11:04:19,132] [INFO] Running command: hmmsearch --tblout GCF_016772315.1_ASM1677231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference/reference_markers.hmm GCF_016772315.1_ASM1677231v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:04:19,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:04:19,434] [INFO] Found 6/6 markers.
[2024-01-24 11:04:19,474] [INFO] Query marker FASTA was written to GCF_016772315.1_ASM1677231v1_genomic.fna/markers.fasta
[2024-01-24 11:04:19,474] [INFO] Task started: Blastn
[2024-01-24 11:04:19,475] [INFO] Running command: blastn -query GCF_016772315.1_ASM1677231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference/reference_markers.fasta -out GCF_016772315.1_ASM1677231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:20,109] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:20,113] [INFO] Selected 11 target genomes.
[2024-01-24 11:04:20,113] [INFO] Target genome list was writen to GCF_016772315.1_ASM1677231v1_genomic.fna/target_genomes.txt
[2024-01-24 11:04:20,133] [INFO] Task started: fastANI
[2024-01-24 11:04:20,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg034430a1-b914-4d9f-9462-5dea8ad5533f/GCF_016772315.1_ASM1677231v1_genomic.fna.gz --refList GCF_016772315.1_ASM1677231v1_genomic.fna/target_genomes.txt --output GCF_016772315.1_ASM1677231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:04:30,018] [INFO] Task succeeded: fastANI
[2024-01-24 11:04:30,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:04:30,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:04:30,031] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:04:30,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:04:30,031] [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
Thiothrix subterranea	strain=Ku-5	GCA_016772315.1	2735563	2735563	type	True	100.0	1356	1357	95	conclusive
Thiothrix winogradskyi	strain=CT3	GCA_021650935.1	96472	96472	type	True	89.2911	981	1357	95	below_threshold
Thiothrix caldifontis	strain=DSM 21228	GCA_900107695.1	525918	525918	type	True	86.7942	888	1357	95	below_threshold
Thiothrix fructosivorans	strain=ATCC 49748	GCA_017349355.1	111770	111770	type	True	84.7246	842	1357	95	below_threshold
Thiothrix unzii	strain=A1	GCA_017901175.1	111769	111769	type	True	84.0389	594	1357	95	below_threshold
Thiothrix litoralis	strain=AS	GCA_017901135.1	2891210	2891210	type	True	82.1208	805	1357	95	below_threshold
Thiothrix lacustris	strain=DSM 21227	GCA_000621325.1	525917	525917	type	True	81.7167	708	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:04:30,033] [INFO] DFAST Taxonomy check result was written to GCF_016772315.1_ASM1677231v1_genomic.fna/tc_result.tsv
[2024-01-24 11:04:30,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:04:30,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:04:30,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference/checkm_data
[2024-01-24 11:04:30,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:04:30,080] [INFO] Task started: CheckM
[2024-01-24 11:04:30,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016772315.1_ASM1677231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016772315.1_ASM1677231v1_genomic.fna/checkm_input GCF_016772315.1_ASM1677231v1_genomic.fna/checkm_result
[2024-01-24 11:05:15,787] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:15,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:15,808] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:15,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:15,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016772315.1_ASM1677231v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:15,809] [INFO] Task started: Blastn
[2024-01-24 11:05:15,809] [INFO] Running command: blastn -query GCF_016772315.1_ASM1677231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa815121-f240-4040-af19-031ed088f4e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016772315.1_ASM1677231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:16,720] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:16,725] [INFO] Selected 9 target genomes.
[2024-01-24 11:05:16,725] [INFO] Target genome list was writen to GCF_016772315.1_ASM1677231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:16,749] [INFO] Task started: fastANI
[2024-01-24 11:05:16,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg034430a1-b914-4d9f-9462-5dea8ad5533f/GCF_016772315.1_ASM1677231v1_genomic.fna.gz --refList GCF_016772315.1_ASM1677231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016772315.1_ASM1677231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:25,227] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:25,236] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:25,236] [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_016772315.1	s__Thiothrix sp016772315	100.0	1356	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107695.1	s__Thiothrix caldifontis	86.7944	888	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349355.1	s__Thiothrix fructosivorans	84.6819	846	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017901175.1	s__Thiothrix unzii	84.0163	594	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017901155.1	s__Thiothrix sp017901155	83.1051	570	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017901135.1	s__Thiothrix sp017901135	82.0874	807	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621325.1	s__Thiothrix lacustris	81.721	710	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425225.1	s__Thiothrix moscowensis	79.9935	516	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	99.11	97.35	0.95	0.89	4	-
GCA_018822845.1	s__Thiothrix sp018822845	79.492	479	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	99.95	99.95	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:25,237] [INFO] GTDB search result was written to GCF_016772315.1_ASM1677231v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:25,238] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:25,241] [INFO] DFAST_QC result json was written to GCF_016772315.1_ASM1677231v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:25,241] [INFO] DFAST_QC completed!
[2024-01-24 11:05:25,241] [INFO] Total running time: 0h1m22s