[2024-01-24 13:40:34,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference
[2024-01-24 13:40:35,568] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,569] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,569] [INFO] Running command: gunzip -c /var/lib/cwl/stgeab0eda0-40ef-4c80-bfd1-b26d37904249/GCF_011682075.1_ASM1168207v1_genomic.fna.gz | prodigal -d GCF_011682075.1_ASM1168207v1_genomic.fna/cds.fna -a GCF_011682075.1_ASM1168207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,303] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,303] [INFO] Running command: hmmsearch --tblout GCF_011682075.1_ASM1168207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference/reference_markers.hmm GCF_011682075.1_ASM1168207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,616] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,617] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,655] [INFO] Query marker FASTA was written to GCF_011682075.1_ASM1168207v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,655] [INFO] Task started: Blastn
[2024-01-24 13:40:48,656] [INFO] Running command: blastn -query GCF_011682075.1_ASM1168207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference/reference_markers.fasta -out GCF_011682075.1_ASM1168207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:49,375] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,379] [INFO] Selected 6 target genomes.
[2024-01-24 13:40:49,380] [INFO] Target genome list was writen to GCF_011682075.1_ASM1168207v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,383] [INFO] Task started: fastANI
[2024-01-24 13:40:49,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgeab0eda0-40ef-4c80-bfd1-b26d37904249/GCF_011682075.1_ASM1168207v1_genomic.fna.gz --refList GCF_011682075.1_ASM1168207v1_genomic.fna/target_genomes.txt --output GCF_011682075.1_ASM1168207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:54,882] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:54,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:54,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:54,889] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:54,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:54,890] [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
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	100.0	1013	1036	95	conclusive
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	94.2467	744	1036	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	92.8127	867	1036	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	79.8752	416	1036	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	79.469	411	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:54,891] [INFO] DFAST Taxonomy check result was written to GCF_011682075.1_ASM1168207v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:54,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:54,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:54,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference/checkm_data
[2024-01-24 13:40:54,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:54,943] [INFO] Task started: CheckM
[2024-01-24 13:40:54,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011682075.1_ASM1168207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011682075.1_ASM1168207v1_genomic.fna/checkm_input GCF_011682075.1_ASM1168207v1_genomic.fna/checkm_result
[2024-01-24 13:41:36,428] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:36,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,483] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:36,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:36,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011682075.1_ASM1168207v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:36,484] [INFO] Task started: Blastn
[2024-01-24 13:41:36,484] [INFO] Running command: blastn -query GCF_011682075.1_ASM1168207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg319483b1-ac1d-48ec-abfe-9ccac7d5e74b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011682075.1_ASM1168207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:37,619] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:37,628] [INFO] Selected 6 target genomes.
[2024-01-24 13:41:37,629] [INFO] Target genome list was writen to GCF_011682075.1_ASM1168207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:37,640] [INFO] Task started: fastANI
[2024-01-24 13:41:37,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgeab0eda0-40ef-4c80-bfd1-b26d37904249/GCF_011682075.1_ASM1168207v1_genomic.fna.gz --refList GCF_011682075.1_ASM1168207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011682075.1_ASM1168207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:44,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,861] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:44,861] [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_011682075.1	s__Cupidesulfovibrio liaohensis	100.0	1013	1036	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015731765.1	s__Cupidesulfovibrio oxamicus	94.2817	742	1036	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021385.1	s__Cupidesulfovibrio vulgaris_A	93.9957	876	1036	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	97.08	97.08	0.92	0.92	2	-
GCF_000504305.1	s__Cupidesulfovibrio termitidis	92.8409	865	1036	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	98.21	98.21	0.92	0.92	2	-
GCF_000226255.1	s__Cupidesulfovibrio sp000226255	91.0801	815	1036	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	96.66	96.06	0.89	0.84	6	-
GCF_000195755.1	s__Nitratidesulfovibrio vulgaris	79.8795	415	1036	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Nitratidesulfovibrio	95.0	99.25	98.85	0.97	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,863] [INFO] GTDB search result was written to GCF_011682075.1_ASM1168207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:44,864] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:44,866] [INFO] DFAST_QC result json was written to GCF_011682075.1_ASM1168207v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:44,867] [INFO] DFAST_QC completed!
[2024-01-24 13:41:44,867] [INFO] Total running time: 0h1m11s