[2024-01-25 20:03:05,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,551] [INFO] DQC Reference Directory: /var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference
[2024-01-25 20:03:06,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,704] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f9dca71-cfd6-47a3-8660-134bc7ea5692/GCF_001592285.1_ASM159228v1_genomic.fna.gz | prodigal -d GCF_001592285.1_ASM159228v1_genomic.fna/cds.fna -a GCF_001592285.1_ASM159228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:19,735] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:19,735] [INFO] Task started: HMMsearch
[2024-01-25 20:03:19,735] [INFO] Running command: hmmsearch --tblout GCF_001592285.1_ASM159228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference/reference_markers.hmm GCF_001592285.1_ASM159228v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:19,989] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:19,990] [INFO] Found 6/6 markers.
[2024-01-25 20:03:20,033] [INFO] Query marker FASTA was written to GCF_001592285.1_ASM159228v1_genomic.fna/markers.fasta
[2024-01-25 20:03:20,033] [INFO] Task started: Blastn
[2024-01-25 20:03:20,033] [INFO] Running command: blastn -query GCF_001592285.1_ASM159228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference/reference_markers.fasta -out GCF_001592285.1_ASM159228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:20,972] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:20,975] [INFO] Selected 15 target genomes.
[2024-01-25 20:03:20,975] [INFO] Target genome list was writen to GCF_001592285.1_ASM159228v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:20,995] [INFO] Task started: fastANI
[2024-01-25 20:03:20,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f9dca71-cfd6-47a3-8660-134bc7ea5692/GCF_001592285.1_ASM159228v1_genomic.fna.gz --refList GCF_001592285.1_ASM159228v1_genomic.fna/target_genomes.txt --output GCF_001592285.1_ASM159228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:36,766] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:36,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:36,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:36,776] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:36,776] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:36,776] [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 pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	100.0	1474	1477	95	conclusive
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	93.37	1258	1477	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	84.5786	1050	1477	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	84.4654	1037	1477	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	83.1819	819	1477	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	83.0735	844	1477	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	82.8458	820	1477	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	82.3061	812	1477	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	82.253	795	1477	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	82.2317	823	1477	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.5947	639	1477	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.1781	690	1477	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	80.1291	602	1477	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.0107	728	1477	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.9271	464	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:36,778] [INFO] DFAST Taxonomy check result was written to GCF_001592285.1_ASM159228v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:36,778] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:36,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:36,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference/checkm_data
[2024-01-25 20:03:36,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:36,823] [INFO] Task started: CheckM
[2024-01-25 20:03:36,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592285.1_ASM159228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592285.1_ASM159228v1_genomic.fna/checkm_input GCF_001592285.1_ASM159228v1_genomic.fna/checkm_result
[2024-01-25 20:05:38,001] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:38,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:38,022] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:38,022] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:38,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592285.1_ASM159228v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:38,023] [INFO] Task started: Blastn
[2024-01-25 20:05:38,023] [INFO] Running command: blastn -query GCF_001592285.1_ASM159228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7c4868d-21d6-4adc-a4e9-a836712c8b9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592285.1_ASM159228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:39,964] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:39,966] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:39,966] [INFO] Target genome list was writen to GCF_001592285.1_ASM159228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:39,989] [INFO] Task started: fastANI
[2024-01-25 20:05:39,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f9dca71-cfd6-47a3-8660-134bc7ea5692/GCF_001592285.1_ASM159228v1_genomic.fna.gz --refList GCF_001592285.1_ASM159228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592285.1_ASM159228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:53,148] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:53,157] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:53,157] [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_001592285.1	s__Hydrogenophaga pseudoflava	100.0	1474	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	97.77	97.69	0.91	0.91	4	conclusive
GCF_001571145.1	s__Hydrogenophaga flava	93.3671	1259	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790705.1	s__Hydrogenophaga sp016790705	86.3757	841	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780075.1	s__Hydrogenophaga sp018780075	85.2318	1082	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	84.5938	1048	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCA_002842215.1	s__Hydrogenophaga sp002842215	84.3865	1076	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823655.1	s__Hydrogenophaga sp013823655	84.1825	580	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018903185.1	s__Hydrogenophaga sp018903185	84.098	472	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.34	99.34	0.82	0.82	2	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	83.27	819	1477	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	83.1881	726	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	82.7729	634	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCA_006227825.1	s__Hydrogenophaga sp006227825	82.7303	589	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	82.4602	716	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227785.1	s__Hydrogenophaga sp006227785	81.524	436	1477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:53,159] [INFO] GTDB search result was written to GCF_001592285.1_ASM159228v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:53,159] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:53,162] [INFO] DFAST_QC result json was written to GCF_001592285.1_ASM159228v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:53,162] [INFO] DFAST_QC completed!
[2024-01-25 20:05:53,162] [INFO] Total running time: 0h2m48s