[2024-01-24 13:57:55,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,535] [INFO] DQC Reference Directory: /var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference
[2024-01-24 13:57:56,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:56,868] [INFO] Task started: Prodigal
[2024-01-24 13:57:56,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg11017fbf-9846-4ea7-9870-d21f7bd0614c/GCF_003417535.1_ASM341753v1_genomic.fna.gz | prodigal -d GCF_003417535.1_ASM341753v1_genomic.fna/cds.fna -a GCF_003417535.1_ASM341753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:13,456] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:13,456] [INFO] Task started: HMMsearch
[2024-01-24 13:58:13,456] [INFO] Running command: hmmsearch --tblout GCF_003417535.1_ASM341753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference/reference_markers.hmm GCF_003417535.1_ASM341753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:13,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:13,789] [INFO] Found 6/6 markers.
[2024-01-24 13:58:13,836] [INFO] Query marker FASTA was written to GCF_003417535.1_ASM341753v1_genomic.fna/markers.fasta
[2024-01-24 13:58:13,837] [INFO] Task started: Blastn
[2024-01-24 13:58:13,837] [INFO] Running command: blastn -query GCF_003417535.1_ASM341753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference/reference_markers.fasta -out GCF_003417535.1_ASM341753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:15,005] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:15,011] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:15,011] [INFO] Target genome list was writen to GCF_003417535.1_ASM341753v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:15,016] [INFO] Task started: fastANI
[2024-01-24 13:58:15,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg11017fbf-9846-4ea7-9870-d21f7bd0614c/GCF_003417535.1_ASM341753v1_genomic.fna.gz --refList GCF_003417535.1_ASM341753v1_genomic.fna/target_genomes.txt --output GCF_003417535.1_ASM341753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:26,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:26,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:26,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:26,841] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:26,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:26,841] [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 borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	100.0	1503	1506	95	conclusive
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	89.7898	1191	1506	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	89.7757	1164	1506	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	89.759	1198	1506	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	87.0675	1054	1506	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.2768	698	1506	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	80.4999	654	1506	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.2349	781	1506	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.2519	527	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:26,843] [INFO] DFAST Taxonomy check result was written to GCF_003417535.1_ASM341753v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:26,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:26,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:26,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference/checkm_data
[2024-01-24 13:58:26,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:26,894] [INFO] Task started: CheckM
[2024-01-24 13:58:26,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003417535.1_ASM341753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003417535.1_ASM341753v1_genomic.fna/checkm_input GCF_003417535.1_ASM341753v1_genomic.fna/checkm_result
[2024-01-24 13:59:44,379] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:44,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:44,400] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:44,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:44,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003417535.1_ASM341753v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:44,401] [INFO] Task started: Blastn
[2024-01-24 13:59:44,402] [INFO] Running command: blastn -query GCF_003417535.1_ASM341753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8b6a03-46d0-42da-b340-6f25366c2f84/dqc_reference/reference_markers_gtdb.fasta -out GCF_003417535.1_ASM341753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:46,633] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:46,637] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:46,637] [INFO] Target genome list was writen to GCF_003417535.1_ASM341753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:46,650] [INFO] Task started: fastANI
[2024-01-24 13:59:46,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg11017fbf-9846-4ea7-9870-d21f7bd0614c/GCF_003417535.1_ASM341753v1_genomic.fna.gz --refList GCF_003417535.1_ASM341753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003417535.1_ASM341753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:55,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:55,166] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:55,167] [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_003417535.1	s__Hydrogenophaga borbori	100.0	1503	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.89	96.31	0.93	0.91	7	conclusive
GCF_000723405.1	s__Hydrogenophaga intermedia	89.8284	1188	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.52	98.31	0.93	0.83	5	-
GCA_011772445.1	s__Hydrogenophaga sp011772445	89.6229	1138	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	9	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	87.0438	1058	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	86.8675	902	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	83.7039	748	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702555.1	s__Ottowia sp016702555	80.5131	660	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.62	99.62	0.96	0.96	2	-
GCA_001724785.1	s__Giesbergeria sp001724785	80.2823	465	1506	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 13:59:55,168] [INFO] GTDB search result was written to GCF_003417535.1_ASM341753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:55,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:55,173] [INFO] DFAST_QC result json was written to GCF_003417535.1_ASM341753v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:55,173] [INFO] DFAST_QC completed!
[2024-01-24 13:59:55,173] [INFO] Total running time: 0h1m60s