[2024-01-24 13:13:39,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference
[2024-01-24 13:13:40,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,815] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,815] [INFO] Running command: gunzip -c /var/lib/cwl/stge8f5510c-b484-425b-8ad1-1d9bb8328407/GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/cds.fna -a GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:49,723] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:49,724] [INFO] Task started: HMMsearch
[2024-01-24 13:13:49,724] [INFO] Running command: hmmsearch --tblout GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference/reference_markers.hmm GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:49,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:49,970] [INFO] Found 6/6 markers.
[2024-01-24 13:13:50,018] [INFO] Query marker FASTA was written to GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:50,019] [INFO] Task started: Blastn
[2024-01-24 13:13:50,019] [INFO] Running command: blastn -query GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference/reference_markers.fasta -out GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:50,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:50,631] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:50,632] [INFO] Target genome list was writen to GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:50,641] [INFO] Task started: fastANI
[2024-01-24 13:13:50,641] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f5510c-b484-425b-8ad1-1d9bb8328407/GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna.gz --refList GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:03,153] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:03,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:03,160] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:03,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:03,161] [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
Desulfofundulus thermosubterraneus	strain=DSM 16057	GCA_900142025.1	348840	348840	type	True	100.0	1082	1089	95	conclusive
Desulfofundulus salinum	strain=435	GCA_003627965.1	2419843	2419843	type	True	92.3843	782	1089	95	below_threshold
Desulfofundulus thermocisternus	strain=DSM 10259	GCA_000686645.1	42471	42471	type	True	84.4657	673	1089	95	below_threshold
Desulfofundulus australicus	strain=DSM 11792	GCA_900129285.1	1566	1566	type	True	84.4081	664	1089	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	77.8442	278	1089	95	below_threshold
Desulfocucumis palustris	strain=NAW-5	GCA_002933875.1	1898651	1898651	type	True	76.0717	60	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,162] [INFO] DFAST Taxonomy check result was written to GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:14:03,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:03,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:03,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference/checkm_data
[2024-01-24 13:14:03,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:03,200] [INFO] Task started: CheckM
[2024-01-24 13:14:03,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/checkm_input GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:14:33,504] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:33,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:33,528] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:33,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:33,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:14:33,529] [INFO] Task started: Blastn
[2024-01-24 13:14:33,529] [INFO] Running command: blastn -query GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ebc0929-481a-4d4f-bc1f-2da1ceb3c8e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:34,358] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:34,362] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:34,362] [INFO] Target genome list was writen to GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:34,372] [INFO] Task started: fastANI
[2024-01-24 13:14:34,372] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f5510c-b484-425b-8ad1-1d9bb8328407/GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna.gz --refList GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:42,985] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:42,993] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:42,993] [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_900142025.1	s__Desulfofundulus thermosubterraneus	100.0	1082	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000214705.1	s__Desulfofundulus kuznetsovii	93.2113	828	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	97.21	97.21	0.77	0.77	2	-
GCF_003627965.1	s__Desulfofundulus salinum	92.3843	782	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129285.1	s__Desulfofundulus australicus	84.3672	666	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	96.88	96.67	0.83	0.80	3	-
GCF_009428905.1	s__Desulfofundulus_A thermobenzoicus	80.8822	488	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus_A	95.0	96.96	95.37	0.88	0.86	3	-
GCF_000429345.1	s__Desulfovirgula thermocuniculi	77.8447	278	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfovirgula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655685.1	s__Desulfotomaculum_G copahuensis	77.2197	227	1089	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfotomaculum_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:42,995] [INFO] GTDB search result was written to GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:42,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:43,004] [INFO] DFAST_QC result json was written to GCF_900142025.1_IMG-taxon_2585428086_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:14:43,004] [INFO] DFAST_QC completed!
[2024-01-24 13:14:43,004] [INFO] Total running time: 0h1m4s