[2024-01-24 14:47:18,978] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:18,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:18,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference
[2024-01-24 14:47:20,230] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:20,231] [INFO] Task started: Prodigal
[2024-01-24 14:47:20,231] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6639d05-d546-4eaa-81d6-ab8195eb58c3/GCF_004365595.1_ASM436559v1_genomic.fna.gz | prodigal -d GCF_004365595.1_ASM436559v1_genomic.fna/cds.fna -a GCF_004365595.1_ASM436559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:32,371] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:32,372] [INFO] Task started: HMMsearch
[2024-01-24 14:47:32,372] [INFO] Running command: hmmsearch --tblout GCF_004365595.1_ASM436559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference/reference_markers.hmm GCF_004365595.1_ASM436559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:32,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:32,822] [INFO] Found 6/6 markers.
[2024-01-24 14:47:32,862] [INFO] Query marker FASTA was written to GCF_004365595.1_ASM436559v1_genomic.fna/markers.fasta
[2024-01-24 14:47:32,862] [INFO] Task started: Blastn
[2024-01-24 14:47:32,862] [INFO] Running command: blastn -query GCF_004365595.1_ASM436559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference/reference_markers.fasta -out GCF_004365595.1_ASM436559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:33,583] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:33,587] [INFO] Selected 7 target genomes.
[2024-01-24 14:47:33,588] [INFO] Target genome list was writen to GCF_004365595.1_ASM436559v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:33,595] [INFO] Task started: fastANI
[2024-01-24 14:47:33,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6639d05-d546-4eaa-81d6-ab8195eb58c3/GCF_004365595.1_ASM436559v1_genomic.fna.gz --refList GCF_004365595.1_ASM436559v1_genomic.fna/target_genomes.txt --output GCF_004365595.1_ASM436559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:42,203] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:42,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:42,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:42,226] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:42,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:42,227] [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	100.0	1306	1308	95	conclusive
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	99.9921	1308	1308	95	conclusive
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	87.0311	982	1308	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	86.5121	981	1308	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	81.5825	724	1308	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	79.0406	515	1308	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	78.6874	463	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:42,229] [INFO] DFAST Taxonomy check result was written to GCF_004365595.1_ASM436559v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:42,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:42,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:42,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference/checkm_data
[2024-01-24 14:47:42,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:42,278] [INFO] Task started: CheckM
[2024-01-24 14:47:42,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365595.1_ASM436559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365595.1_ASM436559v1_genomic.fna/checkm_input GCF_004365595.1_ASM436559v1_genomic.fna/checkm_result
[2024-01-24 14:48:21,173] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:21,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:21,197] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:21,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:21,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365595.1_ASM436559v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:21,198] [INFO] Task started: Blastn
[2024-01-24 14:48:21,199] [INFO] Running command: blastn -query GCF_004365595.1_ASM436559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bb08fc3-d889-4d59-950b-c2c7222e2061/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365595.1_ASM436559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:22,408] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:22,412] [INFO] Selected 7 target genomes.
[2024-01-24 14:48:22,412] [INFO] Target genome list was writen to GCF_004365595.1_ASM436559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:22,416] [INFO] Task started: fastANI
[2024-01-24 14:48:22,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6639d05-d546-4eaa-81d6-ab8195eb58c3/GCF_004365595.1_ASM436559v1_genomic.fna.gz --refList GCF_004365595.1_ASM436559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365595.1_ASM436559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:30,079] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:30,092] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:30,092] [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_001563225.1	s__Pseudodesulfovibrio indicus	99.9921	1308	1308	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000189295.2	s__Pseudodesulfovibrio mercurii	86.9769	986	1308	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	86.5	982	1308	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_017351175.1	s__Pseudodesulfovibrio sp017351175	84.6553	911	1308	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	83.6144	786	1308	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_009762795.1	s__Pseudodesulfovibrio cashew	81.5846	724	1308	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_004025585.1	s__Pseudodesulfovibrio sp004025585	81.3033	727	1308	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:30,097] [INFO] GTDB search result was written to GCF_004365595.1_ASM436559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:30,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:30,102] [INFO] DFAST_QC result json was written to GCF_004365595.1_ASM436559v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:30,102] [INFO] DFAST_QC completed!
[2024-01-24 14:48:30,102] [INFO] Total running time: 0h1m11s