[2024-01-25 19:40:35,517] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:35,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:35,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference
[2024-01-25 19:40:36,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:36,640] [INFO] Task started: Prodigal
[2024-01-25 19:40:36,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg183879b6-c4e5-4466-a0da-d6a4fe833693/GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/cds.fna -a GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:45,091] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:45,091] [INFO] Task started: HMMsearch
[2024-01-25 19:40:45,091] [INFO] Running command: hmmsearch --tblout GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference/reference_markers.hmm GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:45,330] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:45,331] [INFO] Found 6/6 markers.
[2024-01-25 19:40:45,365] [INFO] Query marker FASTA was written to GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:40:45,365] [INFO] Task started: Blastn
[2024-01-25 19:40:45,365] [INFO] Running command: blastn -query GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference/reference_markers.fasta -out GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:45,950] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:45,953] [INFO] Selected 23 target genomes.
[2024-01-25 19:40:45,953] [INFO] Target genome list was writen to GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:40:45,963] [INFO] Task started: fastANI
[2024-01-25 19:40:45,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg183879b6-c4e5-4466-a0da-d6a4fe833693/GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna.gz --refList GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:59,747] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:59,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:59,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:59,754] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:40:59,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:59,754] [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 eikelboomii	strain=ATCC 49788	GCA_900167255.1	92487	92487	type	True	100.0	1358	1362	95	conclusive
Thiothrix winogradskyi	strain=CT3	GCA_021650935.1	96472	96472	type	True	80.3775	121	1362	95	below_threshold
Thiothrix fructosivorans	strain=ATCC 49748	GCA_017349355.1	111770	111770	type	True	79.7539	101	1362	95	below_threshold
Thiothrix subterranea	strain=Ku-5	GCA_016772315.1	2735563	2735563	type	True	79.5697	114	1362	95	below_threshold
Thiothrix unzii	strain=A1	GCA_017901175.1	111769	111769	type	True	79.0346	92	1362	95	below_threshold
Thiolinea disciformis	strain=DSM 14473	GCA_000371925.1	125614	125614	type	True	77.279	212	1362	95	below_threshold
Thiofilum flexile	strain=DSM 14609	GCA_000380185.1	125627	125627	type	True	76.3569	118	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:59,755] [INFO] DFAST Taxonomy check result was written to GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:40:59,756] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:59,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:59,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference/checkm_data
[2024-01-25 19:40:59,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:59,796] [INFO] Task started: CheckM
[2024-01-25 19:40:59,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/checkm_input GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:41:28,778] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:28,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:28,795] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:28,796] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:28,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:41:28,796] [INFO] Task started: Blastn
[2024-01-25 19:41:28,796] [INFO] Running command: blastn -query GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c30ce1e-87b1-4656-a29f-721fe6e591d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:29,775] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:29,777] [INFO] Selected 22 target genomes.
[2024-01-25 19:41:29,778] [INFO] Target genome list was writen to GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:29,805] [INFO] Task started: fastANI
[2024-01-25 19:41:29,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg183879b6-c4e5-4466-a0da-d6a4fe833693/GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna.gz --refList GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:43,479] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:43,485] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:43,485] [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_900167255.1	s__Thiolinea eikelboomii	100.0	1358	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017349355.1	s__Thiothrix fructosivorans	79.7503	100	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015155.1	s__Thiolinea sp008015155	79.4833	659	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822845.1	s__Thiothrix sp018822845	77.8375	52	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix	95.0	99.95	99.95	0.96	0.95	3	-
GCA_016711335.1	s__Thiofilum sp016711335	77.3538	124	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000371925.1	s__Thiolinea disciformis	77.2003	211	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747435.1	s__Thiolinea sp002747435	76.781	86	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380185.1	s__Thiofilum flexile	76.3569	118	1362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiofilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:43,486] [INFO] GTDB search result was written to GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:43,487] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:43,493] [INFO] DFAST_QC result json was written to GCF_900167255.1_IMG-taxon_2585428147_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:41:43,493] [INFO] DFAST_QC completed!
[2024-01-25 19:41:43,493] [INFO] Total running time: 0h1m8s