[2024-01-24 11:20:04,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,124] [INFO] DQC Reference Directory: /var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference
[2024-01-24 11:20:05,281] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,282] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg5972e00a-e3e0-448a-ad80-b0f10eed51ab/GCF_016583655.1_ASM1658365v1_genomic.fna.gz | prodigal -d GCF_016583655.1_ASM1658365v1_genomic.fna/cds.fna -a GCF_016583655.1_ASM1658365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:21,177] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:21,177] [INFO] Task started: HMMsearch
[2024-01-24 11:20:21,177] [INFO] Running command: hmmsearch --tblout GCF_016583655.1_ASM1658365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference/reference_markers.hmm GCF_016583655.1_ASM1658365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:21,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:21,413] [INFO] Found 6/6 markers.
[2024-01-24 11:20:21,450] [INFO] Query marker FASTA was written to GCF_016583655.1_ASM1658365v1_genomic.fna/markers.fasta
[2024-01-24 11:20:21,450] [INFO] Task started: Blastn
[2024-01-24 11:20:21,450] [INFO] Running command: blastn -query GCF_016583655.1_ASM1658365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference/reference_markers.fasta -out GCF_016583655.1_ASM1658365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:22,270] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:22,273] [INFO] Selected 12 target genomes.
[2024-01-24 11:20:22,274] [INFO] Target genome list was writen to GCF_016583655.1_ASM1658365v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:22,284] [INFO] Task started: fastANI
[2024-01-24 11:20:22,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg5972e00a-e3e0-448a-ad80-b0f10eed51ab/GCF_016583655.1_ASM1658365v1_genomic.fna.gz --refList GCF_016583655.1_ASM1658365v1_genomic.fna/target_genomes.txt --output GCF_016583655.1_ASM1658365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:32,186] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:32,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:32,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:32,197] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:32,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:32,197] [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=DSM 10138	GCA_016583655.1	28066	28066	type	True	100.0	1418	1420	95	conclusive
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	99.9995	1418	1420	95	conclusive
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	80.923	723	1420	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	80.8726	736	1420	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.9387	479	1420	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.8332	474	1420	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.3561	340	1420	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.2494	412	1420	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.1692	341	1420	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.7814	295	1420	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.6291	332	1420	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	77.3097	255	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:32,199] [INFO] DFAST Taxonomy check result was written to GCF_016583655.1_ASM1658365v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:32,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:32,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:32,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference/checkm_data
[2024-01-24 11:20:32,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:32,239] [INFO] Task started: CheckM
[2024-01-24 11:20:32,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583655.1_ASM1658365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583655.1_ASM1658365v1_genomic.fna/checkm_input GCF_016583655.1_ASM1658365v1_genomic.fna/checkm_result
[2024-01-24 11:21:27,117] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:27,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:27,135] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:27,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:27,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583655.1_ASM1658365v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:27,136] [INFO] Task started: Blastn
[2024-01-24 11:21:27,136] [INFO] Running command: blastn -query GCF_016583655.1_ASM1658365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5915446-6d77-4834-a73b-a532d608fa53/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583655.1_ASM1658365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:28,673] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:28,676] [INFO] Selected 8 target genomes.
[2024-01-24 11:21:28,676] [INFO] Target genome list was writen to GCF_016583655.1_ASM1658365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:28,683] [INFO] Task started: fastANI
[2024-01-24 11:21:28,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg5972e00a-e3e0-448a-ad80-b0f10eed51ab/GCF_016583655.1_ASM1658365v1_genomic.fna.gz --refList GCF_016583655.1_ASM1658365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583655.1_ASM1658365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:36,571] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:36,579] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:36,579] [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	99.9995	1418	1420	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	93.8681	1157	1420	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	93.1037	1168	1420	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	82.1319	859	1420	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	81.7087	796	1420	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	80.9495	720	1420	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	79.8289	411	1420	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	78.5339	400	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.78	99.78	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:36,580] [INFO] GTDB search result was written to GCF_016583655.1_ASM1658365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:36,581] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:36,584] [INFO] DFAST_QC result json was written to GCF_016583655.1_ASM1658365v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:36,584] [INFO] DFAST_QC completed!
[2024-01-24 11:21:36,584] [INFO] Total running time: 0h1m32s