[2024-01-24 14:46:34,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:34,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:34,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference
[2024-01-24 14:46:35,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:35,574] [INFO] Task started: Prodigal
[2024-01-24 14:46:35,574] [INFO] Running command: gunzip -c /var/lib/cwl/stg15a90d88-ef04-4c1a-8714-c8821d5d043a/GCF_026000375.1_ASM2600037v1_genomic.fna.gz | prodigal -d GCF_026000375.1_ASM2600037v1_genomic.fna/cds.fna -a GCF_026000375.1_ASM2600037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:46,959] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:46,960] [INFO] Task started: HMMsearch
[2024-01-24 14:46:46,960] [INFO] Running command: hmmsearch --tblout GCF_026000375.1_ASM2600037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference/reference_markers.hmm GCF_026000375.1_ASM2600037v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:47,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:47,246] [INFO] Found 6/6 markers.
[2024-01-24 14:46:47,279] [INFO] Query marker FASTA was written to GCF_026000375.1_ASM2600037v1_genomic.fna/markers.fasta
[2024-01-24 14:46:47,279] [INFO] Task started: Blastn
[2024-01-24 14:46:47,279] [INFO] Running command: blastn -query GCF_026000375.1_ASM2600037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference/reference_markers.fasta -out GCF_026000375.1_ASM2600037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:47,989] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:47,992] [INFO] Selected 7 target genomes.
[2024-01-24 14:46:47,993] [INFO] Target genome list was writen to GCF_026000375.1_ASM2600037v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:47,997] [INFO] Task started: fastANI
[2024-01-24 14:46:47,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg15a90d88-ef04-4c1a-8714-c8821d5d043a/GCF_026000375.1_ASM2600037v1_genomic.fna.gz --refList GCF_026000375.1_ASM2600037v1_genomic.fna/target_genomes.txt --output GCF_026000375.1_ASM2600037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:54,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:54,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:54,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:54,317] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:46:54,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:46:54,317] [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=J2	GCA_001563225.1	1716143	1716143	type	True	83.6983	824	1134	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	83.6436	833	1134	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	83.502	810	1134	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	83.4987	807	1134	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	81.5368	625	1134	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	79.6927	540	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:46:54,319] [INFO] DFAST Taxonomy check result was written to GCF_026000375.1_ASM2600037v1_genomic.fna/tc_result.tsv
[2024-01-24 14:46:54,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:54,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:54,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference/checkm_data
[2024-01-24 14:46:54,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:54,363] [INFO] Task started: CheckM
[2024-01-24 14:46:54,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026000375.1_ASM2600037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026000375.1_ASM2600037v1_genomic.fna/checkm_input GCF_026000375.1_ASM2600037v1_genomic.fna/checkm_result
[2024-01-24 14:47:30,636] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:30,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:30,686] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:30,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:30,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026000375.1_ASM2600037v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:30,687] [INFO] Task started: Blastn
[2024-01-24 14:47:30,688] [INFO] Running command: blastn -query GCF_026000375.1_ASM2600037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40ca5063-becb-49a6-97f0-e0f660485a01/dqc_reference/reference_markers_gtdb.fasta -out GCF_026000375.1_ASM2600037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:31,818] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:31,822] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:31,822] [INFO] Target genome list was writen to GCF_026000375.1_ASM2600037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:31,835] [INFO] Task started: fastANI
[2024-01-24 14:47:31,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg15a90d88-ef04-4c1a-8714-c8821d5d043a/GCF_026000375.1_ASM2600037v1_genomic.fna.gz --refList GCF_026000375.1_ASM2600037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026000375.1_ASM2600037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:40,688] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:40,702] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:47:40,703] [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
GCA_015709315.1	s__Pseudodesulfovibrio sp015709315	86.1647	824	1134	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_001563225.1	s__Pseudodesulfovibrio indicus	83.704	823	1134	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_001874525.1	s__Pseudodesulfovibrio hydrargyri	83.4992	807	1134	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	83.4912	810	1134	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	82.2758	740	1134	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	81.5297	625	1134	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	81.1446	662	1134	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_004025585.1	s__Pseudodesulfovibrio sp004025585	81.0686	679	1134	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 14:47:40,704] [INFO] GTDB search result was written to GCF_026000375.1_ASM2600037v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:40,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:40,709] [INFO] DFAST_QC result json was written to GCF_026000375.1_ASM2600037v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:40,709] [INFO] DFAST_QC completed!
[2024-01-24 14:47:40,709] [INFO] Total running time: 0h1m6s