[2023-06-29 09:02:17,928] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:17,934] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:17,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference
[2023-06-29 09:02:19,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:19,269] [INFO] Task started: Prodigal
[2023-06-29 09:02:19,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg704e421e-b22f-4be4-a9ee-1b645f79596d/GCA_020253265.1_ASM2025326v1_genomic.fna.gz | prodigal -d GCA_020253265.1_ASM2025326v1_genomic.fna/cds.fna -a GCA_020253265.1_ASM2025326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:27,306] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:27,307] [INFO] Task started: HMMsearch
[2023-06-29 09:02:27,307] [INFO] Running command: hmmsearch --tblout GCA_020253265.1_ASM2025326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference/reference_markers.hmm GCA_020253265.1_ASM2025326v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:27,554] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:27,556] [INFO] Found 6/6 markers.
[2023-06-29 09:02:27,583] [INFO] Query marker FASTA was written to GCA_020253265.1_ASM2025326v1_genomic.fna/markers.fasta
[2023-06-29 09:02:27,583] [INFO] Task started: Blastn
[2023-06-29 09:02:27,583] [INFO] Running command: blastn -query GCA_020253265.1_ASM2025326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference/reference_markers.fasta -out GCA_020253265.1_ASM2025326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:28,556] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:28,560] [INFO] Selected 29 target genomes.
[2023-06-29 09:02:28,560] [INFO] Target genome list was writen to GCA_020253265.1_ASM2025326v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:28,567] [INFO] Task started: fastANI
[2023-06-29 09:02:28,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg704e421e-b22f-4be4-a9ee-1b645f79596d/GCA_020253265.1_ASM2025326v1_genomic.fna.gz --refList GCA_020253265.1_ASM2025326v1_genomic.fna/target_genomes.txt --output GCA_020253265.1_ASM2025326v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:02:57,132] [INFO] Task succeeded: fastANI
[2023-06-29 09:02:57,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:02:57,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:02:57,159] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:02:57,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:02:57,160] [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
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	79.705	476	870	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	77.6993	279	870	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.6651	291	870	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.6315	239	870	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.6278	285	870	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	77.5271	219	870	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	77.5069	293	870	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	77.4686	214	870	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.3743	268	870	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.2877	205	870	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.2682	262	870	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	77.2229	232	870	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	77.2109	233	870	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.149	180	870	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.1036	189	870	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.034	230	870	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	76.9699	241	870	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.9573	189	870	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.9315	196	870	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	76.9291	145	870	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.9078	210	870	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	76.869	230	870	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	76.7689	197	870	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.744	214	870	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.7088	185	870	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	76.6616	165	870	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	76.6613	166	870	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	76.5952	169	870	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	76.5827	181	870	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:02:57,162] [INFO] DFAST Taxonomy check result was written to GCA_020253265.1_ASM2025326v1_genomic.fna/tc_result.tsv
[2023-06-29 09:02:57,163] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:02:57,163] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:02:57,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference/checkm_data
[2023-06-29 09:02:57,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:02:57,197] [INFO] Task started: CheckM
[2023-06-29 09:02:57,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020253265.1_ASM2025326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020253265.1_ASM2025326v1_genomic.fna/checkm_input GCA_020253265.1_ASM2025326v1_genomic.fna/checkm_result
[2023-06-29 09:03:29,414] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:29,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:29,436] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:29,437] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:29,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020253265.1_ASM2025326v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:29,438] [INFO] Task started: Blastn
[2023-06-29 09:03:29,438] [INFO] Running command: blastn -query GCA_020253265.1_ASM2025326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bafe159-1a1b-4d06-a48e-2611a2c64f5a/dqc_reference/reference_markers_gtdb.fasta -out GCA_020253265.1_ASM2025326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:31,210] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:31,214] [INFO] Selected 19 target genomes.
[2023-06-29 09:03:31,215] [INFO] Target genome list was writen to GCA_020253265.1_ASM2025326v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:31,263] [INFO] Task started: fastANI
[2023-06-29 09:03:31,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg704e421e-b22f-4be4-a9ee-1b645f79596d/GCA_020253265.1_ASM2025326v1_genomic.fna.gz --refList GCA_020253265.1_ASM2025326v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020253265.1_ASM2025326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:03:47,663] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:47,691] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:03:47,692] [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
GCA_002928875.1	s__Rhabdaerophilum sp002928875	85.9783	628	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302635.1	s__Rhabdaerophilum sp017302635	80.5378	540	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008641065.1	s__Rhabdaerophilum calidifontis	79.6927	478	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773635.1	s__Rhabdaerophilum sp009773635	78.8395	424	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009846685.1	s__Rhabdaerophilum sp009846685	78.7649	393	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256205.1	s__Rhabdaerophilum sp002256205	78.4784	393	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735695.1	s__Microvirga zambiensis	77.5246	220	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.2471	264	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	77.1493	180	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383585.1	s__Microvirga sp018383585	77.0203	200	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390695.1	s__Ancylobacter_B sonchi	77.0127	232	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013178945.1	s__Bradyrhizobium sp013178945	76.9426	195	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.74	98.70	0.95	0.95	3	-
GCF_000429045.1	s__Salinarimonas rosea	76.9081	210	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058325.1	s__Methylobacterium currus	76.8491	232	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935205.1	s__Rhodopseudomonas palustris_E	76.7738	138	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	76.7241	187	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	76.6882	164	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	76.6524	204	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	76.372	115	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:03:47,694] [INFO] GTDB search result was written to GCA_020253265.1_ASM2025326v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:03:47,694] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:03:47,712] [INFO] DFAST_QC result json was written to GCA_020253265.1_ASM2025326v1_genomic.fna/dqc_result.json
[2023-06-29 09:03:47,713] [INFO] DFAST_QC completed!
[2023-06-29 09:03:47,713] [INFO] Total running time: 0h1m30s