[2023-06-27 07:56:32,929] [INFO] DFAST_QC pipeline started.
[2023-06-27 07:56:32,931] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 07:56:32,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference
[2023-06-27 07:56:34,169] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 07:56:34,170] [INFO] Task started: Prodigal
[2023-06-27 07:56:34,171] [INFO] Running command: gunzip -c /var/lib/cwl/stga6ba76e5-587f-4be0-8dd6-478165da7d1e/GCA_027494765.1_ASM2749476v1_genomic.fna.gz | prodigal -d GCA_027494765.1_ASM2749476v1_genomic.fna/cds.fna -a GCA_027494765.1_ASM2749476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 07:56:46,831] [INFO] Task succeeded: Prodigal
[2023-06-27 07:56:46,832] [INFO] Task started: HMMsearch
[2023-06-27 07:56:46,832] [INFO] Running command: hmmsearch --tblout GCA_027494765.1_ASM2749476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference/reference_markers.hmm GCA_027494765.1_ASM2749476v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 07:56:47,055] [INFO] Task succeeded: HMMsearch
[2023-06-27 07:56:47,057] [INFO] Found 6/6 markers.
[2023-06-27 07:56:47,090] [INFO] Query marker FASTA was written to GCA_027494765.1_ASM2749476v1_genomic.fna/markers.fasta
[2023-06-27 07:56:47,091] [INFO] Task started: Blastn
[2023-06-27 07:56:47,091] [INFO] Running command: blastn -query GCA_027494765.1_ASM2749476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference/reference_markers.fasta -out GCA_027494765.1_ASM2749476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:56:48,071] [INFO] Task succeeded: Blastn
[2023-06-27 07:56:48,074] [INFO] Selected 21 target genomes.
[2023-06-27 07:56:48,075] [INFO] Target genome list was writen to GCA_027494765.1_ASM2749476v1_genomic.fna/target_genomes.txt
[2023-06-27 07:56:48,076] [INFO] Task started: fastANI
[2023-06-27 07:56:48,077] [INFO] Running command: fastANI --query /var/lib/cwl/stga6ba76e5-587f-4be0-8dd6-478165da7d1e/GCA_027494765.1_ASM2749476v1_genomic.fna.gz --refList GCA_027494765.1_ASM2749476v1_genomic.fna/target_genomes.txt --output GCA_027494765.1_ASM2749476v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 07:57:09,114] [INFO] Task succeeded: fastANI
[2023-06-27 07:57:09,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 07:57:09,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 07:57:09,131] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 07:57:09,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 07:57:09,131] [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
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	82.0357	795	1318	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	82.0003	783	1318	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.958	733	1318	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.8252	676	1318	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	81.0608	596	1318	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.778	581	1318	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.4707	622	1318	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	80.3685	646	1318	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.3409	563	1318	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	80.3157	636	1318	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.2872	619	1318	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	80.1911	592	1318	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.1567	572	1318	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	80.0223	646	1318	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.9273	636	1318	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.8906	721	1318	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.8805	572	1318	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	79.6985	596	1318	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.5392	599	1318	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.4265	546	1318	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.3311	578	1318	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 07:57:09,151] [INFO] DFAST Taxonomy check result was written to GCA_027494765.1_ASM2749476v1_genomic.fna/tc_result.tsv
[2023-06-27 07:57:09,152] [INFO] ===== Taxonomy check completed =====
[2023-06-27 07:57:09,152] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 07:57:09,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference/checkm_data
[2023-06-27 07:57:09,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 07:57:09,206] [INFO] Task started: CheckM
[2023-06-27 07:57:09,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027494765.1_ASM2749476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027494765.1_ASM2749476v1_genomic.fna/checkm_input GCA_027494765.1_ASM2749476v1_genomic.fna/checkm_result
[2023-06-27 07:57:53,375] [INFO] Task succeeded: CheckM
[2023-06-27 07:57:53,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 07:57:53,396] [INFO] ===== Completeness check finished =====
[2023-06-27 07:57:53,397] [INFO] ===== Start GTDB Search =====
[2023-06-27 07:57:53,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027494765.1_ASM2749476v1_genomic.fna/markers.fasta)
[2023-06-27 07:57:53,397] [INFO] Task started: Blastn
[2023-06-27 07:57:53,397] [INFO] Running command: blastn -query GCA_027494765.1_ASM2749476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg537080ab-8446-4872-b91e-dd51111d8a00/dqc_reference/reference_markers_gtdb.fasta -out GCA_027494765.1_ASM2749476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:57:55,332] [INFO] Task succeeded: Blastn
[2023-06-27 07:57:55,336] [INFO] Selected 11 target genomes.
[2023-06-27 07:57:55,336] [INFO] Target genome list was writen to GCA_027494765.1_ASM2749476v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 07:57:55,342] [INFO] Task started: fastANI
[2023-06-27 07:57:55,342] [INFO] Running command: fastANI --query /var/lib/cwl/stga6ba76e5-587f-4be0-8dd6-478165da7d1e/GCA_027494765.1_ASM2749476v1_genomic.fna.gz --refList GCA_027494765.1_ASM2749476v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027494765.1_ASM2749476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 07:58:07,970] [INFO] Task succeeded: fastANI
[2023-06-27 07:58:07,980] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 07:58:07,980] [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_013363755.1	s__Comamonas antarcticus	96.7805	1221	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014204315.1	s__Comamonas konjaci_A	90.8052	1158	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706035.1	s__Comamonas sp902706035	87.423	1018	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413525.1	s__Comamonas sp018413525	87.2683	1040	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598795.1	s__Comamonas acidovorans	81.9633	787	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	97.72	96.19	0.89	0.80	41	-
GCF_001544075.1	s__Comamonas terrae	81.9158	737	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	81.4862	629	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_003604195.1	s__Giesbergeria lacusdiani	81.2757	594	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	80.9443	659	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_003053545.1	s__Acidovorax sp003053545	80.8673	767	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_014302995.1	s__Variovorax sp014302995	79.3447	621	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 07:58:07,982] [INFO] GTDB search result was written to GCA_027494765.1_ASM2749476v1_genomic.fna/result_gtdb.tsv
[2023-06-27 07:58:07,982] [INFO] ===== GTDB Search completed =====
[2023-06-27 07:58:07,986] [INFO] DFAST_QC result json was written to GCA_027494765.1_ASM2749476v1_genomic.fna/dqc_result.json
[2023-06-27 07:58:07,986] [INFO] DFAST_QC completed!
[2023-06-27 07:58:07,986] [INFO] Total running time: 0h1m35s