[2024-01-24 14:22:58,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:58,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:58,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference
[2024-01-24 14:23:01,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:01,559] [INFO] Task started: Prodigal
[2024-01-24 14:23:01,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeee771f-ae77-4c76-995d-9f67d78b0c25/GCF_003843835.1_ASM384383v1_genomic.fna.gz | prodigal -d GCF_003843835.1_ASM384383v1_genomic.fna/cds.fna -a GCF_003843835.1_ASM384383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:11,163] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:11,164] [INFO] Task started: HMMsearch
[2024-01-24 14:23:11,164] [INFO] Running command: hmmsearch --tblout GCF_003843835.1_ASM384383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference/reference_markers.hmm GCF_003843835.1_ASM384383v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:11,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:11,603] [INFO] Found 6/6 markers.
[2024-01-24 14:23:11,646] [INFO] Query marker FASTA was written to GCF_003843835.1_ASM384383v1_genomic.fna/markers.fasta
[2024-01-24 14:23:11,647] [INFO] Task started: Blastn
[2024-01-24 14:23:11,647] [INFO] Running command: blastn -query GCF_003843835.1_ASM384383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference/reference_markers.fasta -out GCF_003843835.1_ASM384383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:16,077] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:16,083] [INFO] Selected 26 target genomes.
[2024-01-24 14:23:16,084] [INFO] Target genome list was writen to GCF_003843835.1_ASM384383v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:16,100] [INFO] Task started: fastANI
[2024-01-24 14:23:16,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeee771f-ae77-4c76-995d-9f67d78b0c25/GCF_003843835.1_ASM384383v1_genomic.fna.gz --refList GCF_003843835.1_ASM384383v1_genomic.fna/target_genomes.txt --output GCF_003843835.1_ASM384383v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:38,219] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:38,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:38,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:38,348] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:38,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:38,349] [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 crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.6531	458	906	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.1367	364	906	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	79.0796	365	906	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	79.0561	414	906	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	79.0543	408	906	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	79.0244	412	906	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.9857	378	906	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	78.9267	277	906	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	78.9174	448	906	95	below_threshold
Extensimonas vulgaris	strain=CGMCC 1.10977	GCA_007830535.1	1031594	1031594	type	True	78.8746	373	906	95	below_threshold
Extensimonas vulgaris	strain=S4	GCA_007996985.1	1031594	1031594	type	True	78.8715	370	906	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.8706	412	906	95	below_threshold
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	78.8468	374	906	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	78.7777	376	906	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	78.7639	372	906	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	78.6093	364	906	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	78.6004	377	906	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	78.594	383	906	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	78.4859	317	906	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	78.4687	377	906	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.4666	324	906	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.4032	389	906	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.3315	355	906	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	78.113	301	906	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.9003	264	906	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	77.8724	256	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:38,352] [INFO] DFAST Taxonomy check result was written to GCF_003843835.1_ASM384383v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:38,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:38,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:38,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference/checkm_data
[2024-01-24 14:23:38,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:38,452] [INFO] Task started: CheckM
[2024-01-24 14:23:38,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003843835.1_ASM384383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003843835.1_ASM384383v1_genomic.fna/checkm_input GCF_003843835.1_ASM384383v1_genomic.fna/checkm_result
[2024-01-24 14:24:26,298] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:26,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:26,324] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:26,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:26,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003843835.1_ASM384383v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:26,326] [INFO] Task started: Blastn
[2024-01-24 14:24:26,326] [INFO] Running command: blastn -query GCF_003843835.1_ASM384383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81a269d-779c-444e-aa98-a765312d322b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003843835.1_ASM384383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:28,483] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:28,488] [INFO] Selected 23 target genomes.
[2024-01-24 14:24:28,488] [INFO] Target genome list was writen to GCF_003843835.1_ASM384383v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:28,517] [INFO] Task started: fastANI
[2024-01-24 14:24:28,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeee771f-ae77-4c76-995d-9f67d78b0c25/GCF_003843835.1_ASM384383v1_genomic.fna.gz --refList GCF_003843835.1_ASM384383v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003843835.1_ASM384383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:49,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:49,477] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:49,478] [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_003843835.1	s__Tibeticola sediminis	100.0	905	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013693755.1	s__Tibeticola sp013693755	83.7138	650	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCA_005503335.1	s__SCMQ01 sp005503335	79.9344	454	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	79.6649	457	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_015159745.1	s__Ramlibacter aquaticus	79.2553	385	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.95	0.95	2	-
GCF_003604195.1	s__Giesbergeria lacusdiani	79.2255	419	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	79.2129	409	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCA_016721925.1	s__JAABQG01 sp016721925	79.1567	448	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCF_012932145.1	s__Giesbergeria sp012932145	79.0766	407	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_016428875.1	s__Xylophilus sp016428875	79.0694	382	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	79.0295	423	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_014874145.1	s__Ramlibacter sp014874145	78.9732	394	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	78.9002	414	906	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_001580455.1	s__Ramlibacter tataouinensis_B	78.8202	386	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241405.1	s__Alicycliphilus sp018241405	78.7878	357	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCA_017307855.1	s__JAGOCV01 sp017307855	78.7835	369	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	78.743	279	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002176815.1	s__Acidovorax sp002176815	78.6648	371	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCF_900104515.1	s__Acidovorax_A cattleyae	78.6162	364	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	78.4588	380	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	78.2935	383	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	77.6747	376	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063435.1	s__Limnohabitans_A sp003063435	77.6747	256	906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:49,489] [INFO] GTDB search result was written to GCF_003843835.1_ASM384383v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:49,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:49,497] [INFO] DFAST_QC result json was written to GCF_003843835.1_ASM384383v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:49,497] [INFO] DFAST_QC completed!
[2024-01-24 14:24:49,497] [INFO] Total running time: 0h1m51s