[2024-01-24 14:12:14,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:14,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:14,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference
[2024-01-24 14:12:15,653] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:15,654] [INFO] Task started: Prodigal
[2024-01-24 14:12:15,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg87bdde2c-3854-4875-bf26-ec6b3a9553e8/GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/cds.fna -a GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:27,707] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:27,708] [INFO] Task started: HMMsearch
[2024-01-24 14:12:27,708] [INFO] Running command: hmmsearch --tblout GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference/reference_markers.hmm GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:28,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:28,011] [INFO] Found 6/6 markers.
[2024-01-24 14:12:28,051] [INFO] Query marker FASTA was written to GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:28,051] [INFO] Task started: Blastn
[2024-01-24 14:12:28,051] [INFO] Running command: blastn -query GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference/reference_markers.fasta -out GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:28,773] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:28,777] [INFO] Selected 13 target genomes.
[2024-01-24 14:12:28,778] [INFO] Target genome list was writen to GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:28,784] [INFO] Task started: fastANI
[2024-01-24 14:12:28,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg87bdde2c-3854-4875-bf26-ec6b3a9553e8/GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna.gz --refList GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:37,963] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:37,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:37,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:37,977] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:37,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:37,977] [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
Desulfacinum hydrothermale	strain=DSM 13146	GCA_900176285.1	109258	109258	type	True	100.0	1201	1201	95	conclusive
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	82.9306	869	1201	95	below_threshold
Desulfoglaeba alkanexedens	strain=ALDC	GCA_005377625.1	361111	361111	type	True	76.9939	215	1201	95	below_threshold
Desulfosoma caldarium	strain=DSM 22027	GCA_003751385.1	610254	610254	type	True	76.9686	222	1201	95	below_threshold
Syntrophobacter fumaroxidans	strain=MPOB	GCA_000014965.1	119484	119484	type	True	76.4958	82	1201	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	76.1665	64	1201	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	76.1126	59	1201	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	76.0703	63	1201	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	75.8584	58	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:37,979] [INFO] DFAST Taxonomy check result was written to GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:37,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:37,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:37,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference/checkm_data
[2024-01-24 14:12:37,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:38,022] [INFO] Task started: CheckM
[2024-01-24 14:12:38,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/checkm_input GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:16,381] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:16,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:16,404] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:16,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:16,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:16,405] [INFO] Task started: Blastn
[2024-01-24 14:13:16,405] [INFO] Running command: blastn -query GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb039d355-0b89-4875-841b-14ef1166ceff/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:17,588] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:17,607] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:17,608] [INFO] Target genome list was writen to GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:17,675] [INFO] Task started: fastANI
[2024-01-24 14:13:17,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg87bdde2c-3854-4875-bf26-ec6b3a9553e8/GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna.gz --refList GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:26,379] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:26,396] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:26,397] [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_900176285.1	s__Desulfacinum hydrothermale	100.0	1201	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014359885.1	s__Desulfacinum sp014359885	83.0661	882	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129305.1	s__Desulfacinum infernum	82.9211	870	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011329395.1	s__Desulfosoma infernum_A	77.8594	338	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751385.1	s__Desulfosoma caldarium	76.9579	223	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005377625.1	s__Desulfoglaeba alkanexedens	76.9068	214	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfoglaeba	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873705.1	s__CG2-30-61-12 sp001873705	76.4196	146	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__CG2-30-61-12	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014965.1	s__Syntrophobacter fumaroxidans	76.3067	81	1201	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__Syntrophobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979235.1	s__Dissulfurirhabdus thermomarina	76.1948	63	1201	d__Bacteria;p__Desulfobacterota;c__Dissulfuribacteria;o__Dissulfuribacterales;f__Dissulfurirhabdaceae;g__Dissulfurirhabdus	95.0	99.96	99.96	0.96	0.96	2	-
GCA_011390035.1	s__JAABTE01 sp011390035	75.9495	62	1201	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:26,398] [INFO] GTDB search result was written to GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:26,399] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:26,402] [INFO] DFAST_QC result json was written to GCF_900176285.1_IMG-taxon_2585428172_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:26,402] [INFO] DFAST_QC completed!
[2024-01-24 14:13:26,402] [INFO] Total running time: 0h1m12s