[2024-01-25 18:16:50,752] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:50,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:50,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference
[2024-01-25 18:16:51,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:51,924] [INFO] Task started: Prodigal
[2024-01-25 18:16:51,924] [INFO] Running command: gunzip -c /var/lib/cwl/stg9743c0c0-ac14-41f4-aacd-d27b2ee4b489/GCF_013340305.1_ASM1334030v1_genomic.fna.gz | prodigal -d GCF_013340305.1_ASM1334030v1_genomic.fna/cds.fna -a GCF_013340305.1_ASM1334030v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:03,818] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:03,819] [INFO] Task started: HMMsearch
[2024-01-25 18:17:03,819] [INFO] Running command: hmmsearch --tblout GCF_013340305.1_ASM1334030v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference/reference_markers.hmm GCF_013340305.1_ASM1334030v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:04,069] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:04,069] [INFO] Found 6/6 markers.
[2024-01-25 18:17:04,096] [INFO] Query marker FASTA was written to GCF_013340305.1_ASM1334030v1_genomic.fna/markers.fasta
[2024-01-25 18:17:04,096] [INFO] Task started: Blastn
[2024-01-25 18:17:04,096] [INFO] Running command: blastn -query GCF_013340305.1_ASM1334030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference/reference_markers.fasta -out GCF_013340305.1_ASM1334030v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:04,657] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:04,660] [INFO] Selected 18 target genomes.
[2024-01-25 18:17:04,660] [INFO] Target genome list was writen to GCF_013340305.1_ASM1334030v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:04,667] [INFO] Task started: fastANI
[2024-01-25 18:17:04,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg9743c0c0-ac14-41f4-aacd-d27b2ee4b489/GCF_013340305.1_ASM1334030v1_genomic.fna.gz --refList GCF_013340305.1_ASM1334030v1_genomic.fna/target_genomes.txt --output GCF_013340305.1_ASM1334030v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:17,224] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:17,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:17,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:17,231] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:17:17,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:17,231] [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
Desulfovibrio psychrotolerans	strain=JS1	GCA_013340305.1	415242	415242	type	True	100.0	1246	1247	95	conclusive
Desulfovibrio subterraneus	strain=HN2	GCA_013340285.1	2718620	2718620	type	True	79.7118	621	1247	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.9101	260	1247	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.8872	254	1247	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.6705	311	1247	95	below_threshold
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	77.0966	214	1247	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	76.9619	91	1247	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	76.8138	131	1247	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	76.6002	117	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:17,233] [INFO] DFAST Taxonomy check result was written to GCF_013340305.1_ASM1334030v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:17,233] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:17,233] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:17,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference/checkm_data
[2024-01-25 18:17:17,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:17,273] [INFO] Task started: CheckM
[2024-01-25 18:17:17,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340305.1_ASM1334030v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340305.1_ASM1334030v1_genomic.fna/checkm_input GCF_013340305.1_ASM1334030v1_genomic.fna/checkm_result
[2024-01-25 18:17:52,552] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:52,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:52,571] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:52,571] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:52,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340305.1_ASM1334030v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:52,572] [INFO] Task started: Blastn
[2024-01-25 18:17:52,572] [INFO] Running command: blastn -query GCF_013340305.1_ASM1334030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b262810-f26d-4ffc-b1be-c88ec983dd95/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340305.1_ASM1334030v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:53,459] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:53,462] [INFO] Selected 19 target genomes.
[2024-01-25 18:17:53,462] [INFO] Target genome list was writen to GCF_013340305.1_ASM1334030v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:53,492] [INFO] Task started: fastANI
[2024-01-25 18:17:53,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg9743c0c0-ac14-41f4-aacd-d27b2ee4b489/GCF_013340305.1_ASM1334030v1_genomic.fna.gz --refList GCF_013340305.1_ASM1334030v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013340305.1_ASM1334030v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:04,832] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:04,840] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:04,841] [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_013340305.1	s__Halodesulfovibrio psychrotolerans	100.0	1246	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013340285.1	s__Halodesulfovibrio subterraneus	79.7246	619	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252375.1	s__Halodesulfovibrio sp003252375	79.6242	533	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Halodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682075.1	s__Cupidesulfovibrio liaohensis	77.885	262	1247	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_015731765.1	s__Cupidesulfovibrio oxamicus	77.8425	258	1247	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	77.6831	309	1247	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	77.6276	314	1247	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	77.56	309	1247	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_001311825.1	s__Pseudodesulfovibrio brasiliensis	76.7335	119	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022125.1	s__Desulfovibrio desulfuricans_A	76.6438	92	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.36	99.22	0.93	0.89	5	-
GCA_019114025.1	s__Bilophila faecipullorum	76.5974	64	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	99.16	98.64	0.81	0.70	3	-
GCA_004796465.1	s__MADRE1 sp004796465	76.533	62	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__MADRE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575755.1	s__Desulfovibrio sp910575755	76.424	92	1247	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:18:04,842] [INFO] GTDB search result was written to GCF_013340305.1_ASM1334030v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:04,843] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:04,845] [INFO] DFAST_QC result json was written to GCF_013340305.1_ASM1334030v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:04,845] [INFO] DFAST_QC completed!
[2024-01-25 18:18:04,846] [INFO] Total running time: 0h1m14s