[2024-01-24 13:48:59,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference
[2024-01-24 13:49:01,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,322] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,322] [INFO] Running command: gunzip -c /var/lib/cwl/stga4af75a2-9cc8-4001-84e5-82eb45ff2a83/GCF_000430005.1_ASM43000v1_genomic.fna.gz | prodigal -d GCF_000430005.1_ASM43000v1_genomic.fna/cds.fna -a GCF_000430005.1_ASM43000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:13,915] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:13,916] [INFO] Task started: HMMsearch
[2024-01-24 13:49:13,916] [INFO] Running command: hmmsearch --tblout GCF_000430005.1_ASM43000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference/reference_markers.hmm GCF_000430005.1_ASM43000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,177] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,206] [INFO] Query marker FASTA was written to GCF_000430005.1_ASM43000v1_genomic.fna/markers.fasta
[2024-01-24 13:49:14,207] [INFO] Task started: Blastn
[2024-01-24 13:49:14,207] [INFO] Running command: blastn -query GCF_000430005.1_ASM43000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference/reference_markers.fasta -out GCF_000430005.1_ASM43000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:14,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:14,831] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:14,831] [INFO] Target genome list was writen to GCF_000430005.1_ASM43000v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:14,838] [INFO] Task started: fastANI
[2024-01-24 13:49:14,839] [INFO] Running command: fastANI --query /var/lib/cwl/stga4af75a2-9cc8-4001-84e5-82eb45ff2a83/GCF_000430005.1_ASM43000v1_genomic.fna.gz --refList GCF_000430005.1_ASM43000v1_genomic.fna/target_genomes.txt --output GCF_000430005.1_ASM43000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:29,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:29,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:29,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:29,112] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:29,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:29,112] [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 cuneatus	strain=DSM 11391	GCA_000430005.1	159728	159728	type	True	99.9999	1075	1082	95	conclusive
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	76.6962	61	1082	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	76.318	73	1082	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	76.0654	59	1082	95	below_threshold
Oleidesulfovibrio alaskensis	strain=DSM 16109	GCA_000482745.1	58180	58180	type	True	75.9217	54	1082	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	75.7892	61	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:29,114] [INFO] DFAST Taxonomy check result was written to GCF_000430005.1_ASM43000v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:29,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:29,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:29,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference/checkm_data
[2024-01-24 13:49:29,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:29,151] [INFO] Task started: CheckM
[2024-01-24 13:49:29,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430005.1_ASM43000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430005.1_ASM43000v1_genomic.fna/checkm_input GCF_000430005.1_ASM43000v1_genomic.fna/checkm_result
[2024-01-24 13:50:07,558] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:07,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:07,579] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:07,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:07,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430005.1_ASM43000v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:07,580] [INFO] Task started: Blastn
[2024-01-24 13:50:07,580] [INFO] Running command: blastn -query GCF_000430005.1_ASM43000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e2435ba-0dc7-4deb-bccb-a1946d190c3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430005.1_ASM43000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:08,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:08,469] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:08,470] [INFO] Target genome list was writen to GCF_000430005.1_ASM43000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:08,499] [INFO] Task started: fastANI
[2024-01-24 13:50:08,499] [INFO] Running command: fastANI --query /var/lib/cwl/stga4af75a2-9cc8-4001-84e5-82eb45ff2a83/GCF_000430005.1_ASM43000v1_genomic.fna.gz --refList GCF_000430005.1_ASM43000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430005.1_ASM43000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:21,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:21,136] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:21,137] [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_000430005.1	s__Frigididesulfovibrio cuneatus	99.9999	1075	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Frigididesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014202345.1	s__Desulfovibrio intestinalis	76.3873	58	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002237645.1	s__Desulfovibrio sp002237645	76.3454	61	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504305.1	s__Cupidesulfovibrio termitidis	76.3441	72	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	98.21	98.21	0.92	0.92	2	-
GCA_002293605.1	s__Frigididesulfovibrio sp002293605	76.1713	62	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Frigididesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682075.1	s__Cupidesulfovibrio liaohensis	76.0935	58	1082	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_000226255.1	s__Cupidesulfovibrio sp000226255	76.0642	68	1082	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_000021385.1	s__Cupidesulfovibrio vulgaris_A	76.0182	65	1082	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_000482745.1	s__Oleidesulfovibrio alaskensis	75.9335	52	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Oleidesulfovibrio	95.0	99.29	99.19	0.96	0.95	4	-
GCF_900102485.1	s__Desulfovibrio legallii_A	75.7615	71	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.86	99.86	0.97	0.97	2	-
GCF_000420465.1	s__Desulfovibrio desulfuricans	75.6763	71	1082	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.33	95.61	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,138] [INFO] GTDB search result was written to GCF_000430005.1_ASM43000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:21,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:21,142] [INFO] DFAST_QC result json was written to GCF_000430005.1_ASM43000v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:21,142] [INFO] DFAST_QC completed!
[2024-01-24 13:50:21,142] [INFO] Total running time: 0h1m21s