[2024-01-24 13:45:45,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference
[2024-01-24 13:45:47,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,039] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaddc91a-1021-4bca-a930-21f90960e064/GCF_009762795.1_ASM976279v1_genomic.fna.gz | prodigal -d GCF_009762795.1_ASM976279v1_genomic.fna/cds.fna -a GCF_009762795.1_ASM976279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:59,767] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:59,767] [INFO] Task started: HMMsearch
[2024-01-24 13:45:59,767] [INFO] Running command: hmmsearch --tblout GCF_009762795.1_ASM976279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference/reference_markers.hmm GCF_009762795.1_ASM976279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:00,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:00,080] [INFO] Found 6/6 markers.
[2024-01-24 13:46:00,115] [INFO] Query marker FASTA was written to GCF_009762795.1_ASM976279v1_genomic.fna/markers.fasta
[2024-01-24 13:46:00,115] [INFO] Task started: Blastn
[2024-01-24 13:46:00,115] [INFO] Running command: blastn -query GCF_009762795.1_ASM976279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference/reference_markers.fasta -out GCF_009762795.1_ASM976279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:00,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:00,767] [INFO] Selected 10 target genomes.
[2024-01-24 13:46:00,768] [INFO] Target genome list was writen to GCF_009762795.1_ASM976279v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:00,774] [INFO] Task started: fastANI
[2024-01-24 13:46:00,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaddc91a-1021-4bca-a930-21f90960e064/GCF_009762795.1_ASM976279v1_genomic.fna.gz --refList GCF_009762795.1_ASM976279v1_genomic.fna/target_genomes.txt --output GCF_009762795.1_ASM976279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:09,254] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:09,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:09,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:09,264] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:09,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:09,264] [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 cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	100.0	1302	1303	95	conclusive
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	81.5771	723	1303	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	81.5666	732	1303	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	81.5148	725	1303	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	81.4668	742	1303	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	80.576	627	1303	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	79.6709	522	1303	95	below_threshold
Pseudodesulfovibrio profundus	strain=500-1	GCA_900217235.1	57320	57320	type	True	79.1565	381	1303	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	79.0491	445	1303	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	78.5292	391	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:09,266] [INFO] DFAST Taxonomy check result was written to GCF_009762795.1_ASM976279v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:09,266] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:09,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:09,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference/checkm_data
[2024-01-24 13:46:09,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:09,311] [INFO] Task started: CheckM
[2024-01-24 13:46:09,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009762795.1_ASM976279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009762795.1_ASM976279v1_genomic.fna/checkm_input GCF_009762795.1_ASM976279v1_genomic.fna/checkm_result
[2024-01-24 13:46:49,206] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:49,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:49,231] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:49,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:49,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009762795.1_ASM976279v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:49,233] [INFO] Task started: Blastn
[2024-01-24 13:46:49,233] [INFO] Running command: blastn -query GCF_009762795.1_ASM976279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4484b5c9-9e9b-47ce-ab49-21b6ce16d526/dqc_reference/reference_markers_gtdb.fasta -out GCF_009762795.1_ASM976279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:50,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:50,193] [INFO] Selected 10 target genomes.
[2024-01-24 13:46:50,194] [INFO] Target genome list was writen to GCF_009762795.1_ASM976279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:50,219] [INFO] Task started: fastANI
[2024-01-24 13:46:50,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaddc91a-1021-4bca-a930-21f90960e064/GCF_009762795.1_ASM976279v1_genomic.fna.gz --refList GCF_009762795.1_ASM976279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009762795.1_ASM976279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:59,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:59,699] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:59,700] [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_009762795.1	s__Pseudodesulfovibrio cashew	100.0	1303	1303	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_001563225.1	s__Pseudodesulfovibrio indicus	81.5857	721	1303	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000189295.2	s__Pseudodesulfovibrio mercurii	81.5277	724	1303	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	81.4471	745	1303	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	81.1882	605	1303	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	80.6168	637	1303	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_000176915.2	s__Pseudodesulfovibrio aespoeensis	80.5458	630	1303	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.98	99.94	1.00	0.98	8	-
GCF_012516435.1	s__Pseudodesulfovibrio sp012516435	79.7219	477	1303	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_009729555.1	s__Pseudodesulfovibrio sp009729555	79.6869	520	1303	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_900217235.1	s__Pseudodesulfovibrio profundus	79.1921	382	1303	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	98.02	97.98	0.88	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:59,703] [INFO] GTDB search result was written to GCF_009762795.1_ASM976279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:59,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:59,712] [INFO] DFAST_QC result json was written to GCF_009762795.1_ASM976279v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:59,712] [INFO] DFAST_QC completed!
[2024-01-24 13:46:59,712] [INFO] Total running time: 0h1m14s