[2024-01-24 15:18:51,103] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference
[2024-01-24 15:18:52,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,606] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eca4356-d799-404a-9ce9-164cf98c47b7/GCF_005938115.1_ASM593811v1_genomic.fna.gz | prodigal -d GCF_005938115.1_ASM593811v1_genomic.fna/cds.fna -a GCF_005938115.1_ASM593811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:09,926] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:09,926] [INFO] Task started: HMMsearch
[2024-01-24 15:19:09,926] [INFO] Running command: hmmsearch --tblout GCF_005938115.1_ASM593811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference/reference_markers.hmm GCF_005938115.1_ASM593811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:10,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:10,289] [INFO] Found 6/6 markers.
[2024-01-24 15:19:10,344] [INFO] Query marker FASTA was written to GCF_005938115.1_ASM593811v1_genomic.fna/markers.fasta
[2024-01-24 15:19:10,345] [INFO] Task started: Blastn
[2024-01-24 15:19:10,345] [INFO] Running command: blastn -query GCF_005938115.1_ASM593811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference/reference_markers.fasta -out GCF_005938115.1_ASM593811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:11,455] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:11,459] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:11,459] [INFO] Target genome list was writen to GCF_005938115.1_ASM593811v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:11,463] [INFO] Task started: fastANI
[2024-01-24 15:19:11,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eca4356-d799-404a-9ce9-164cf98c47b7/GCF_005938115.1_ASM593811v1_genomic.fna.gz --refList GCF_005938115.1_ASM593811v1_genomic.fna/target_genomes.txt --output GCF_005938115.1_ASM593811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:22,811] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:22,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:22,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:22,820] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:19:22,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:22,821] [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
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	100.0	1678	1679	95	conclusive
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	99.9677	1602	1679	95	conclusive
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	99.9586	1623	1679	95	conclusive
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	89.6576	1207	1679	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	86.3843	1055	1679	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.8185	694	1679	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.7769	454	1679	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.4253	617	1679	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.3233	532	1679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:22,825] [INFO] DFAST Taxonomy check result was written to GCF_005938115.1_ASM593811v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:22,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:22,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:22,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference/checkm_data
[2024-01-24 15:19:22,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:22,881] [INFO] Task started: CheckM
[2024-01-24 15:19:22,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005938115.1_ASM593811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005938115.1_ASM593811v1_genomic.fna/checkm_input GCF_005938115.1_ASM593811v1_genomic.fna/checkm_result
[2024-01-24 15:20:46,416] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:46,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:46,443] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:46,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:46,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005938115.1_ASM593811v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:46,445] [INFO] Task started: Blastn
[2024-01-24 15:20:46,445] [INFO] Running command: blastn -query GCF_005938115.1_ASM593811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66643f71-a4a7-498f-b2ff-075439e0a924/dqc_reference/reference_markers_gtdb.fasta -out GCF_005938115.1_ASM593811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:48,612] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:48,615] [INFO] Selected 8 target genomes.
[2024-01-24 15:20:48,616] [INFO] Target genome list was writen to GCF_005938115.1_ASM593811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:48,633] [INFO] Task started: fastANI
[2024-01-24 15:20:48,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eca4356-d799-404a-9ce9-164cf98c47b7/GCF_005938115.1_ASM593811v1_genomic.fna.gz --refList GCF_005938115.1_ASM593811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005938115.1_ASM593811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:57,903] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:57,911] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:57,912] [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_000723405.1	s__Hydrogenophaga intermedia	99.9586	1623	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.52	98.31	0.93	0.83	5	conclusive
GCA_011772445.1	s__Hydrogenophaga sp011772445	92.2897	1266	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	9	-
GCF_003417535.1	s__Hydrogenophaga borbori	89.6702	1206	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.89	96.31	0.93	0.91	7	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	86.8526	909	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	86.4051	1053	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	83.3048	739	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	80.8606	713	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	80.0922	441	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:57,913] [INFO] GTDB search result was written to GCF_005938115.1_ASM593811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:57,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:57,917] [INFO] DFAST_QC result json was written to GCF_005938115.1_ASM593811v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:57,917] [INFO] DFAST_QC completed!
[2024-01-24 15:20:57,917] [INFO] Total running time: 0h2m7s