[2024-01-24 14:13:18,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,629] [INFO] DQC Reference Directory: /var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference
[2024-01-24 14:13:20,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:20,010] [INFO] Task started: Prodigal
[2024-01-24 14:13:20,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a1da9cb-fe5e-43fa-8ea5-cd9779221ca7/GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/cds.fna -a GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:23,741] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:23,741] [INFO] Task started: HMMsearch
[2024-01-24 14:13:23,741] [INFO] Running command: hmmsearch --tblout GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference/reference_markers.hmm GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:23,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:23,989] [INFO] Found 6/6 markers.
[2024-01-24 14:13:24,017] [INFO] Query marker FASTA was written to GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:13:24,017] [INFO] Task started: Blastn
[2024-01-24 14:13:24,018] [INFO] Running command: blastn -query GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference/reference_markers.fasta -out GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:24,622] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:24,626] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:24,627] [INFO] Target genome list was writen to GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:13:24,638] [INFO] Task started: fastANI
[2024-01-24 14:13:24,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1da9cb-fe5e-43fa-8ea5-cd9779221ca7/GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna.gz --refList GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:30,450] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:30,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:30,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:30,457] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:30,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:30,458] [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
Marinitoga hydrogenitolerans	strain=DSM 16785	GCA_900129175.1	287990	287990	type	True	100.0	729	730	95	conclusive
Marinitoga lauensis	strain=LG1	GCA_004135675.1	2201189	2201189	type	True	80.8283	510	730	95	below_threshold
Marinitoga litoralis	strain=DSM 21709	GCA_016908145.1	570855	570855	type	True	79.9954	429	730	95	below_threshold
Marinitoga piezophila	strain=KA3	GCA_000255135.1	149715	149715	type	True	78.7952	348	730	95	below_threshold
Tepiditoga spiralis	strain=sy52	GCA_014701195.1	2108365	2108365	type	True	75.4931	152	730	95	below_threshold
Fusobacterium varium	strain=NCTC10560	GCA_900637705.1	856	856	type	True	74.6429	67	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:30,460] [INFO] DFAST Taxonomy check result was written to GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:13:30,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:30,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:30,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference/checkm_data
[2024-01-24 14:13:30,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:30,487] [INFO] Task started: CheckM
[2024-01-24 14:13:30,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/checkm_input GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:50,164] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:50,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:50,194] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:50,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:50,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:50,195] [INFO] Task started: Blastn
[2024-01-24 14:13:50,196] [INFO] Running command: blastn -query GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7387ad7-6b28-4df9-b515-20eaab072f48/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:51,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:51,136] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:51,136] [INFO] Target genome list was writen to GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:51,160] [INFO] Task started: fastANI
[2024-01-24 14:13:51,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1da9cb-fe5e-43fa-8ea5-cd9779221ca7/GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna.gz --refList GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:56,292] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:56,298] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:56,299] [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_900129175.1	s__Marinitoga hydrogenitolerans	100.0	729	730	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001021165.1	s__Marinitoga sp001021165	83.926	514	730	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	96.86	96.83	0.88	0.88	3	-
GCF_004135675.1	s__Marinitoga lauensis	80.8304	510	730	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057715.1	s__Marinitoga sp011057715	80.3211	411	730	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908145.1	s__Marinitoga litoralis	80.0077	428	730	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255135.1	s__Marinitoga piezophila	78.7664	351	730	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	99.22	99.16	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:56,300] [INFO] GTDB search result was written to GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:56,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:56,305] [INFO] DFAST_QC result json was written to GCF_900129175.1_IMG-taxon_2585428042_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:56,306] [INFO] DFAST_QC completed!
[2024-01-24 14:13:56,306] [INFO] Total running time: 0h0m38s