[2024-01-25 18:53:20,436] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:20,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:20,442] [INFO] DQC Reference Directory: /var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference
[2024-01-25 18:53:21,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:21,590] [INFO] Task started: Prodigal
[2024-01-25 18:53:21,590] [INFO] Running command: gunzip -c /var/lib/cwl/stg2800df32-f3ed-4638-b721-bc551734f1b2/GCF_002017865.1_ASM201786v1_genomic.fna.gz | prodigal -d GCF_002017865.1_ASM201786v1_genomic.fna/cds.fna -a GCF_002017865.1_ASM201786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:36,422] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:36,423] [INFO] Task started: HMMsearch
[2024-01-25 18:53:36,423] [INFO] Running command: hmmsearch --tblout GCF_002017865.1_ASM201786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference/reference_markers.hmm GCF_002017865.1_ASM201786v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:36,758] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:36,759] [INFO] Found 6/6 markers.
[2024-01-25 18:53:36,797] [INFO] Query marker FASTA was written to GCF_002017865.1_ASM201786v1_genomic.fna/markers.fasta
[2024-01-25 18:53:36,797] [INFO] Task started: Blastn
[2024-01-25 18:53:36,797] [INFO] Running command: blastn -query GCF_002017865.1_ASM201786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference/reference_markers.fasta -out GCF_002017865.1_ASM201786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:37,592] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:37,595] [INFO] Selected 12 target genomes.
[2024-01-25 18:53:37,595] [INFO] Target genome list was writen to GCF_002017865.1_ASM201786v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:37,604] [INFO] Task started: fastANI
[2024-01-25 18:53:37,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg2800df32-f3ed-4638-b721-bc551734f1b2/GCF_002017865.1_ASM201786v1_genomic.fna.gz --refList GCF_002017865.1_ASM201786v1_genomic.fna/target_genomes.txt --output GCF_002017865.1_ASM201786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:48,005] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:48,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:48,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:48,014] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:48,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:48,014] [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
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	100.0	1477	1488	95	conclusive
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	99.9738	1416	1488	95	conclusive
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	80.9814	734	1488	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	80.9595	730	1488	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.8374	492	1488	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.7283	490	1488	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.5075	335	1488	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.2578	431	1488	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.9323	348	1488	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.6298	305	1488	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.5438	332	1488	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	77.2209	258	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:48,016] [INFO] DFAST Taxonomy check result was written to GCF_002017865.1_ASM201786v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:48,016] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:48,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:48,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference/checkm_data
[2024-01-25 18:53:48,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:48,058] [INFO] Task started: CheckM
[2024-01-25 18:53:48,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002017865.1_ASM201786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002017865.1_ASM201786v1_genomic.fna/checkm_input GCF_002017865.1_ASM201786v1_genomic.fna/checkm_result
[2024-01-25 18:54:55,763] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:55,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:55,783] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:55,783] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:55,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002017865.1_ASM201786v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:55,784] [INFO] Task started: Blastn
[2024-01-25 18:54:55,784] [INFO] Running command: blastn -query GCF_002017865.1_ASM201786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2989e95-9324-4691-b856-90f7f19d3173/dqc_reference/reference_markers_gtdb.fasta -out GCF_002017865.1_ASM201786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:57,357] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:57,359] [INFO] Selected 8 target genomes.
[2024-01-25 18:54:57,359] [INFO] Target genome list was writen to GCF_002017865.1_ASM201786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:57,368] [INFO] Task started: fastANI
[2024-01-25 18:54:57,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg2800df32-f3ed-4638-b721-bc551734f1b2/GCF_002017865.1_ASM201786v1_genomic.fna.gz --refList GCF_002017865.1_ASM201786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002017865.1_ASM201786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:05,782] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:05,788] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:05,789] [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_002017865.1	s__Rhodoferax fermentans	100.0	1478	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018619435.1	s__Rhodoferax sp018619435	93.8732	1165	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416775.1	s__Rhodoferax sp013416775	93.1307	1183	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083775.1	s__Rhodoferax ferrireducens_A	82.2126	865	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905735.1	s__Rhodoferax sp903905735	81.5941	816	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938565.1	s__Rhodoferax antarcticus	80.9681	729	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.95	0.95	2	-
GCA_011391545.1	s__Rhodoferax sp011391545	79.7047	418	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903856025.1	s__Rhodoferax sp903856025	78.5913	403	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.78	99.78	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:05,790] [INFO] GTDB search result was written to GCF_002017865.1_ASM201786v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:05,791] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:05,794] [INFO] DFAST_QC result json was written to GCF_002017865.1_ASM201786v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:05,794] [INFO] DFAST_QC completed!
[2024-01-25 18:55:05,794] [INFO] Total running time: 0h1m45s