[2024-01-24 14:19:20,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:20,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:20,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference
[2024-01-24 14:19:23,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:23,554] [INFO] Task started: Prodigal
[2024-01-24 14:19:23,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dae4fd6-16f5-4938-8895-e422cab86812/GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/cds.fna -a GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:34,042] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:34,042] [INFO] Task started: HMMsearch
[2024-01-24 14:19:34,042] [INFO] Running command: hmmsearch --tblout GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference/reference_markers.hmm GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:34,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:34,330] [INFO] Found 6/6 markers.
[2024-01-24 14:19:34,376] [INFO] Query marker FASTA was written to GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:34,376] [INFO] Task started: Blastn
[2024-01-24 14:19:34,377] [INFO] Running command: blastn -query GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference/reference_markers.fasta -out GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:35,420] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:35,423] [INFO] Selected 18 target genomes.
[2024-01-24 14:19:35,424] [INFO] Target genome list was writen to GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:35,432] [INFO] Task started: fastANI
[2024-01-24 14:19:35,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dae4fd6-16f5-4938-8895-e422cab86812/GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna.gz --refList GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:50,790] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:50,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:50,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:50,837] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:50,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:50,838] [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
Desulfoscipio geothermicus	strain=DSM 3669	GCA_900115975.1	39060	39060	type	True	100.0	1171	1176	95	conclusive
Desulfotruncus alcoholivorax	strain=DSM 16058	GCA_000430885.1	265477	265477	type	True	78.3629	212	1176	95	below_threshold
Desulfotruncus arcticus	strain=DSM 17038	GCA_900113335.1	341036	341036	type	True	78.3097	225	1176	95	below_threshold
Desulfofundulus salinum	strain=435	GCA_003627965.1	2419843	2419843	type	True	76.836	105	1176	95	below_threshold
Sporotomaculum syntrophicum	strain=FB	GCA_009932395.1	182264	182264	type	True	76.5966	121	1176	95	below_threshold
Desulfofundulus thermosubterraneus	strain=DSM 16057	GCA_900142025.1	348840	348840	type	True	76.4916	102	1176	95	below_threshold
Desulfofundulus thermocisternus	strain=DSM 10259	GCA_000686645.1	42471	42471	type	True	76.2779	94	1176	95	below_threshold
Desulfofundulus australicus	strain=DSM 11792	GCA_900129285.1	1566	1566	type	True	76.0526	93	1176	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	75.9668	76	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:50,840] [INFO] DFAST Taxonomy check result was written to GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:19:50,840] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:50,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:50,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference/checkm_data
[2024-01-24 14:19:50,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:50,900] [INFO] Task started: CheckM
[2024-01-24 14:19:50,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/checkm_input GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:20:27,745] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:27,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,778] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:27,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:27,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:20:27,780] [INFO] Task started: Blastn
[2024-01-24 14:20:27,780] [INFO] Running command: blastn -query GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg42bab8b8-4b83-4eb3-8746-3bd53cc78714/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:30,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:30,222] [INFO] Selected 17 target genomes.
[2024-01-24 14:20:30,222] [INFO] Target genome list was writen to GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:30,241] [INFO] Task started: fastANI
[2024-01-24 14:20:30,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dae4fd6-16f5-4938-8895-e422cab86812/GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna.gz --refList GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:41,942] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:41,969] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:41,969] [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_900115975.1	s__Desulfoscipio geothermicus	100.0	1171	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfoscipio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015594625.1	s__Desulfotruncus sp015594625	80.201	421	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430885.1	s__Desulfotruncus alcoholivorax	78.345	213	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113335.1	s__Desulfotruncus arcticus	78.3088	225	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124625.1	s__Sporotomaculum thermosapovorans	77.8296	270	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000233715.2	s__Sporotomaculum gibsoniae	77.7537	271	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841205.1	s__Sporotomaculum geothermicum_A	77.4138	166	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841645.1	s__Sporotomaculum geothermicum_B	77.0647	135	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781965.1	s__BRH-c8a sp009781965	76.906	74	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__BRH-c8a	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627965.1	s__Desulfofundulus salinum	76.836	105	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841905.1	s__Sporotomaculum geothermicum_C	76.6581	101	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932395.1	s__Sporotomaculum syntrophicum	76.6142	120	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000214705.1	s__Desulfofundulus kuznetsovii	76.5621	121	1176	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_900129285.1	s__Desulfofundulus australicus	76.0526	93	1176	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	96.88	96.67	0.83	0.80	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,971] [INFO] GTDB search result was written to GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:41,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:41,975] [INFO] DFAST_QC result json was written to GCF_900115975.1_IMG-taxon_2602042027_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:20:41,975] [INFO] DFAST_QC completed!
[2024-01-24 14:20:41,975] [INFO] Total running time: 0h1m22s