[2024-01-24 13:32:42,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,124] [INFO] DQC Reference Directory: /var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference
[2024-01-24 13:32:43,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,455] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ea9aeab-7b95-4e1c-90f3-769525f6758a/GCF_000375485.1_ASM37548v1_genomic.fna.gz | prodigal -d GCF_000375485.1_ASM37548v1_genomic.fna/cds.fna -a GCF_000375485.1_ASM37548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:54,432] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:54,432] [INFO] Task started: HMMsearch
[2024-01-24 13:32:54,432] [INFO] Running command: hmmsearch --tblout GCF_000375485.1_ASM37548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference/reference_markers.hmm GCF_000375485.1_ASM37548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:54,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:54,696] [INFO] Found 6/6 markers.
[2024-01-24 13:32:54,726] [INFO] Query marker FASTA was written to GCF_000375485.1_ASM37548v1_genomic.fna/markers.fasta
[2024-01-24 13:32:54,726] [INFO] Task started: Blastn
[2024-01-24 13:32:54,726] [INFO] Running command: blastn -query GCF_000375485.1_ASM37548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference/reference_markers.fasta -out GCF_000375485.1_ASM37548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:55,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:55,382] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:55,382] [INFO] Target genome list was writen to GCF_000375485.1_ASM37548v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:55,399] [INFO] Task started: fastANI
[2024-01-24 13:32:55,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea9aeab-7b95-4e1c-90f3-769525f6758a/GCF_000375485.1_ASM37548v1_genomic.fna.gz --refList GCF_000375485.1_ASM37548v1_genomic.fna/target_genomes.txt --output GCF_000375485.1_ASM37548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:05,182] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:05,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:05,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:05,193] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:05,194] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:05,194] [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
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	78.2383	341	1091	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	78.1074	341	1091	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	77.9924	331	1091	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	77.9625	329	1091	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	77.7948	256	1091	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	77.5913	308	1091	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	77.5599	314	1091	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	77.3672	160	1091	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	77.3524	253	1091	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.7926	114	1091	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	76.6834	120	1091	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	76.6455	157	1091	95	below_threshold
Desulfocurvibacter africanus subsp. africanus	strain=DSM 2603	GCA_000422545.1	1511600	873	type	True	76.5351	131	1091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:05,197] [INFO] DFAST Taxonomy check result was written to GCF_000375485.1_ASM37548v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:05,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:05,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:05,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference/checkm_data
[2024-01-24 13:33:05,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:05,235] [INFO] Task started: CheckM
[2024-01-24 13:33:05,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000375485.1_ASM37548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000375485.1_ASM37548v1_genomic.fna/checkm_input GCF_000375485.1_ASM37548v1_genomic.fna/checkm_result
[2024-01-24 13:33:39,717] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:39,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:39,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:39,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:39,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000375485.1_ASM37548v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:39,737] [INFO] Task started: Blastn
[2024-01-24 13:33:39,737] [INFO] Running command: blastn -query GCF_000375485.1_ASM37548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43a3b79-e4dd-42b6-ab8a-c235054a0a96/dqc_reference/reference_markers_gtdb.fasta -out GCF_000375485.1_ASM37548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:40,590] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:40,593] [INFO] Selected 12 target genomes.
[2024-01-24 13:33:40,593] [INFO] Target genome list was writen to GCF_000375485.1_ASM37548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:40,604] [INFO] Task started: fastANI
[2024-01-24 13:33:40,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea9aeab-7b95-4e1c-90f3-769525f6758a/GCF_000375485.1_ASM37548v1_genomic.fna.gz --refList GCF_000375485.1_ASM37548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000375485.1_ASM37548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:48,136] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:48,144] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:48,145] [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_000375485.1	s__Pseudodesulfovibrio oxyclinae	100.0	1083	1091	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001311825.1	s__Pseudodesulfovibrio brasiliensis	81.0587	563	1091	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_008001235.1	s__Pseudodesulfovibrio sp008001235	78.6017	379	1091	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_008830225.1	s__Pseudodesulfovibrio senegalensis	78.2511	288	1091	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_001874525.1	s__Pseudodesulfovibrio hydrargyri	78.0047	330	1091	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_000189295.2	s__Pseudodesulfovibrio mercurii	77.9652	330	1091	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709315.1	s__Pseudodesulfovibrio sp015709315	77.9284	297	1091	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_000420485.1	s__Paucidesulfovibrio longus	77.7814	257	1091	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729555.1	s__Pseudodesulfovibrio sp009729555	77.3346	254	1091	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_900167125.1	s__Paucidesulfovibrio gracilis	77.2004	128	1091	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:48,146] [INFO] GTDB search result was written to GCF_000375485.1_ASM37548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:48,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:48,150] [INFO] DFAST_QC result json was written to GCF_000375485.1_ASM37548v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:48,150] [INFO] DFAST_QC completed!
[2024-01-24 13:33:48,150] [INFO] Total running time: 0h1m6s