[2024-01-25 17:37:05,571] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:05,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:05,573] [INFO] DQC Reference Directory: /var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference
[2024-01-25 17:37:06,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:06,710] [INFO] Task started: Prodigal
[2024-01-25 17:37:06,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg791ceb5e-b409-41b9-8f08-f7dec3ae9ca7/GCF_026283955.1_ASM2628395v1_genomic.fna.gz | prodigal -d GCF_026283955.1_ASM2628395v1_genomic.fna/cds.fna -a GCF_026283955.1_ASM2628395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:23,026] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:23,027] [INFO] Task started: HMMsearch
[2024-01-25 17:37:23,027] [INFO] Running command: hmmsearch --tblout GCF_026283955.1_ASM2628395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference/reference_markers.hmm GCF_026283955.1_ASM2628395v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:23,360] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:23,361] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg791ceb5e-b409-41b9-8f08-f7dec3ae9ca7/GCF_026283955.1_ASM2628395v1_genomic.fna.gz]
[2024-01-25 17:37:23,403] [INFO] Query marker FASTA was written to GCF_026283955.1_ASM2628395v1_genomic.fna/markers.fasta
[2024-01-25 17:37:23,403] [INFO] Task started: Blastn
[2024-01-25 17:37:23,403] [INFO] Running command: blastn -query GCF_026283955.1_ASM2628395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference/reference_markers.fasta -out GCF_026283955.1_ASM2628395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:24,154] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:24,157] [INFO] Selected 14 target genomes.
[2024-01-25 17:37:24,158] [INFO] Target genome list was writen to GCF_026283955.1_ASM2628395v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:24,162] [INFO] Task started: fastANI
[2024-01-25 17:37:24,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg791ceb5e-b409-41b9-8f08-f7dec3ae9ca7/GCF_026283955.1_ASM2628395v1_genomic.fna.gz --refList GCF_026283955.1_ASM2628395v1_genomic.fna/target_genomes.txt --output GCF_026283955.1_ASM2628395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:37,346] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:37,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:37,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:37,356] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:37:37,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:37:37,356] [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
Dyella tabacisoli	strain=L4-6	GCA_003350925.1	2282381	2282381	type	True	83.2876	1059	1652	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.3502	487	1652	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.2963	571	1652	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	79.2409	531	1652	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.1749	558	1652	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.1001	523	1652	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.9843	484	1652	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.7546	565	1652	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.7482	476	1652	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.6488	426	1652	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	78.5942	433	1652	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	78.5815	435	1652	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	78.5811	458	1652	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.9408	202	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:37,371] [INFO] DFAST Taxonomy check result was written to GCF_026283955.1_ASM2628395v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:37,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:37,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:37,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference/checkm_data
[2024-01-25 17:37:37,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:37,430] [INFO] Task started: CheckM
[2024-01-25 17:37:37,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026283955.1_ASM2628395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026283955.1_ASM2628395v1_genomic.fna/checkm_input GCF_026283955.1_ASM2628395v1_genomic.fna/checkm_result
[2024-01-25 17:38:24,474] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:24,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:24,499] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:24,499] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:24,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026283955.1_ASM2628395v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:24,501] [INFO] Task started: Blastn
[2024-01-25 17:38:24,501] [INFO] Running command: blastn -query GCF_026283955.1_ASM2628395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f9b24d-498f-4174-80bc-bb8117eb939c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026283955.1_ASM2628395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:26,021] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:26,024] [INFO] Selected 24 target genomes.
[2024-01-25 17:38:26,024] [INFO] Target genome list was writen to GCF_026283955.1_ASM2628395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:26,036] [INFO] Task started: fastANI
[2024-01-25 17:38:26,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg791ceb5e-b409-41b9-8f08-f7dec3ae9ca7/GCF_026283955.1_ASM2628395v1_genomic.fna.gz --refList GCF_026283955.1_ASM2628395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026283955.1_ASM2628395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:47,158] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:47,172] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:38:47,172] [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_003350925.1	s__Dyella tabacisoli	83.2876	1059	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	79.4725	669	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	79.4301	560	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	79.364	696	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_001010355.1	s__Dyella japonica	79.35	487	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905005.1	s__Dyella kyungheensis	79.305	570	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296575.1	s__Dyella sp004296575	79.246	530	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297575.1	s__Dyella sp014297575	79.2	555	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	79.1691	535	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428975.1	s__Dyella sp016428975	79.1362	557	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725385.1	s__Dyella japonica_C	79.1191	549	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002001165.1	s__Rhodanobacter sp002001165	79.109	495	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	79.1062	510	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264855.1	s__Dyella jiangningensis_C	79.1049	547	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351225.1	s__Dyella solisilvae	79.0734	526	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329435.1	s__Rhodanobacter sp008329435	79.0628	485	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114325.1	s__Rhodanobacter glycinis	79.0474	485	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	97.24	96.89	0.85	0.82	5	-
GCF_002001175.1	s__Rhodanobacter sp002001175	79.0441	517	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002878475.1	s__Dyella sp002878475	78.8961	527	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	78.8267	491	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863405.1	s__Dyella_B sp014863405	78.7921	560	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799035.1	s__Rhodanobacter lindaniclasticus	78.7786	445	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	78.7463	381	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002749725.1	s__Rhodanobacter sp002749725	78.6841	452	1652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.01	98.01	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:47,174] [INFO] GTDB search result was written to GCF_026283955.1_ASM2628395v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:47,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:47,178] [INFO] DFAST_QC result json was written to GCF_026283955.1_ASM2628395v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:47,178] [INFO] DFAST_QC completed!
[2024-01-25 17:38:47,178] [INFO] Total running time: 0h1m42s