[2024-01-25 19:46:35,886] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:35,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:35,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference
[2024-01-25 19:46:36,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:36,981] [INFO] Task started: Prodigal
[2024-01-25 19:46:36,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e0490a0-7b45-4c02-b831-60cd4f234d33/GCF_014641715.1_ASM1464171v1_genomic.fna.gz | prodigal -d GCF_014641715.1_ASM1464171v1_genomic.fna/cds.fna -a GCF_014641715.1_ASM1464171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:49,357] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:49,358] [INFO] Task started: HMMsearch
[2024-01-25 19:46:49,358] [INFO] Running command: hmmsearch --tblout GCF_014641715.1_ASM1464171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference/reference_markers.hmm GCF_014641715.1_ASM1464171v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:49,649] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:49,649] [INFO] Found 6/6 markers.
[2024-01-25 19:46:49,686] [INFO] Query marker FASTA was written to GCF_014641715.1_ASM1464171v1_genomic.fna/markers.fasta
[2024-01-25 19:46:49,686] [INFO] Task started: Blastn
[2024-01-25 19:46:49,686] [INFO] Running command: blastn -query GCF_014641715.1_ASM1464171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference/reference_markers.fasta -out GCF_014641715.1_ASM1464171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:50,579] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:50,582] [INFO] Selected 22 target genomes.
[2024-01-25 19:46:50,582] [INFO] Target genome list was writen to GCF_014641715.1_ASM1464171v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:50,594] [INFO] Task started: fastANI
[2024-01-25 19:46:50,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e0490a0-7b45-4c02-b831-60cd4f234d33/GCF_014641715.1_ASM1464171v1_genomic.fna.gz --refList GCF_014641715.1_ASM1464171v1_genomic.fna/target_genomes.txt --output GCF_014641715.1_ASM1464171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:12,474] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:12,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:12,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:12,489] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:12,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:12,490] [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
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	100.0	1363	1368	95	conclusive
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	80.6963	686	1368	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	80.4237	635	1368	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	79.0503	539	1368	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	78.971	532	1368	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.8995	570	1368	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.8531	565	1368	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.7672	517	1368	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.7565	461	1368	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.7299	524	1368	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.7267	524	1368	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.7107	496	1368	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	78.7024	559	1368	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.6779	405	1368	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.5769	568	1368	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	78.5709	462	1368	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	78.5451	497	1368	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.4453	498	1368	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.3214	528	1368	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	78.2736	425	1368	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	78.26	417	1368	95	below_threshold
Polaromonas vacuolata	strain=KCTC 22033	GCA_012584515.1	37448	37448	type	True	77.374	222	1368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:12,491] [INFO] DFAST Taxonomy check result was written to GCF_014641715.1_ASM1464171v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:12,493] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:12,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:12,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference/checkm_data
[2024-01-25 19:47:12,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:12,550] [INFO] Task started: CheckM
[2024-01-25 19:47:12,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641715.1_ASM1464171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641715.1_ASM1464171v1_genomic.fna/checkm_input GCF_014641715.1_ASM1464171v1_genomic.fna/checkm_result
[2024-01-25 19:47:51,842] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:51,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:51,875] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:51,875] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:51,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641715.1_ASM1464171v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:51,876] [INFO] Task started: Blastn
[2024-01-25 19:47:51,876] [INFO] Running command: blastn -query GCF_014641715.1_ASM1464171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06a9899b-5ff9-47e3-a4e5-722d23618bda/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641715.1_ASM1464171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:53,679] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:53,683] [INFO] Selected 9 target genomes.
[2024-01-25 19:47:53,684] [INFO] Target genome list was writen to GCF_014641715.1_ASM1464171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:53,710] [INFO] Task started: fastANI
[2024-01-25 19:47:53,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e0490a0-7b45-4c02-b831-60cd4f234d33/GCF_014641715.1_ASM1464171v1_genomic.fna.gz --refList GCF_014641715.1_ASM1464171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641715.1_ASM1464171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:04,548] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:04,555] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:04,555] [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_014641715.1	s__Polaromonas eurypsychrophila	100.0	1363	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013824015.1	s__Polaromonas sp013824015	85.7906	870	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817205.1	s__Polaromonas sp013817205	84.4478	870	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379095.1	s__Polaromonas sp002379095	83.7467	928	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379085.1	s__Polaromonas sp002379085	83.5967	947	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002278925.1	s__Polaromonas sp002278925	83.5932	923	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	99.99	99.98	0.99	0.99	5	-
GCF_002001015.1	s__Polaromonas sp002001015	82.1107	848	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282655.1	s__Polaromonas sp000282655	81.3029	770	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711205.1	s__Polaromonas sp003711205	81.2677	755	1368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:04,557] [INFO] GTDB search result was written to GCF_014641715.1_ASM1464171v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:04,558] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:04,564] [INFO] DFAST_QC result json was written to GCF_014641715.1_ASM1464171v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:04,564] [INFO] DFAST_QC completed!
[2024-01-25 19:48:04,564] [INFO] Total running time: 0h1m29s