[2024-01-24 14:05:31,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference
[2024-01-24 14:05:32,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,871] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a022095-2a94-4b97-a145-0eae34c49a06/GCF_000422545.1_ASM42254v1_genomic.fna.gz | prodigal -d GCF_000422545.1_ASM42254v1_genomic.fna/cds.fna -a GCF_000422545.1_ASM42254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:46,572] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:46,573] [INFO] Task started: HMMsearch
[2024-01-24 14:05:46,573] [INFO] Running command: hmmsearch --tblout GCF_000422545.1_ASM42254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference/reference_markers.hmm GCF_000422545.1_ASM42254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:46,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:46,872] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,913] [INFO] Query marker FASTA was written to GCF_000422545.1_ASM42254v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,914] [INFO] Task started: Blastn
[2024-01-24 14:05:46,914] [INFO] Running command: blastn -query GCF_000422545.1_ASM42254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference/reference_markers.fasta -out GCF_000422545.1_ASM42254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:47,615] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:47,618] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:47,618] [INFO] Target genome list was writen to GCF_000422545.1_ASM42254v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:47,624] [INFO] Task started: fastANI
[2024-01-24 14:05:47,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a022095-2a94-4b97-a145-0eae34c49a06/GCF_000422545.1_ASM42254v1_genomic.fna.gz --refList GCF_000422545.1_ASM42254v1_genomic.fna/target_genomes.txt --output GCF_000422545.1_ASM42254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:58,105] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:58,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:58,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:58,117] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:58,117] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:58,117] [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
Desulfocurvibacter africanus subsp. africanus	strain=DSM 2603	GCA_000422545.1	1511600	873	type	True	100.0	1445	1449	95	conclusive
Desulfohalovibrio alkalitolerans	strain=DSM 16529	GCA_000422245.1	293256	293256	type	True	77.8232	271	1449	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	77.7834	271	1449	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	77.3393	229	1449	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	77.2579	229	1449	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	77.2155	245	1449	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	77.2033	272	1449	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	77.1578	240	1449	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.0199	202	1449	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	76.8956	245	1449	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	76.8942	208	1449	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	76.7919	145	1449	95	below_threshold
Solidesulfovibrio aerotolerans	strain=DSM 16695	GCA_009856865.1	295255	295255	type	True	76.6353	146	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:58,119] [INFO] DFAST Taxonomy check result was written to GCF_000422545.1_ASM42254v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:58,119] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:58,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:58,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference/checkm_data
[2024-01-24 14:05:58,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:58,175] [INFO] Task started: CheckM
[2024-01-24 14:05:58,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422545.1_ASM42254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422545.1_ASM42254v1_genomic.fna/checkm_input GCF_000422545.1_ASM42254v1_genomic.fna/checkm_result
[2024-01-24 14:06:40,982] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:40,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,003] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:41,004] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:41,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422545.1_ASM42254v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:41,004] [INFO] Task started: Blastn
[2024-01-24 14:06:41,005] [INFO] Running command: blastn -query GCF_000422545.1_ASM42254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c2ae5fe-5219-4b89-8b02-8839a66ec174/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422545.1_ASM42254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:42,132] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:42,135] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:42,136] [INFO] Target genome list was writen to GCF_000422545.1_ASM42254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:42,172] [INFO] Task started: fastANI
[2024-01-24 14:06:42,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a022095-2a94-4b97-a145-0eae34c49a06/GCF_000422545.1_ASM42254v1_genomic.fna.gz --refList GCF_000422545.1_ASM42254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422545.1_ASM42254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:55,991] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,012] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:56,012] [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_000422545.1	s__Desulfocurvibacter africanus	100.0	1445	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvibacter	95.0	96.43	95.36	0.91	0.90	3	conclusive
GCF_000422205.1	s__Desulfohalovibrio sp000422205	78.016	338	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519125.1	s__Desulfocurvus vexinensis	78.0077	303	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428705.1	s__UBA6079 sp002428705	77.8914	335	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__UBA6079	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422245.1	s__Desulfohalovibrio alkalitolerans	77.8313	271	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711295.1	s__Desulfohalovibrio reitneri	77.8167	269	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422565.1	s__Aminidesulfovibrio aminophilus	77.7485	283	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Aminidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709205.1	s__JACCQO01 sp015709205	77.6426	279	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JACCQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452635.1	s__UBA6814 sp002452635	77.375	252	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__UBA6814	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822105.1	s__Humidesulfovibrio sp018822105	77.3333	272	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002840405.1	s__Humidesulfovibrio sp002840405	77.3058	267	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420485.1	s__Paucidesulfovibrio longus	77.2577	229	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218665.1	s__Humidesulfovibrio sp016218665	77.2098	228	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013019105.1	s__Fundidesulfovibrio sp013019105	77.2007	273	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018817515.1	s__Humidesulfovibrio sp018817515	77.1096	259	1449	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,014] [INFO] GTDB search result was written to GCF_000422545.1_ASM42254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:56,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:56,019] [INFO] DFAST_QC result json was written to GCF_000422545.1_ASM42254v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:56,019] [INFO] DFAST_QC completed!
[2024-01-24 14:06:56,019] [INFO] Total running time: 0h1m24s