[2024-01-24 13:01:10,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:10,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:10,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference
[2024-01-24 13:01:11,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:11,578] [INFO] Task started: Prodigal
[2024-01-24 13:01:11,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg9435cea5-fb10-4711-be46-0e81a7033b98/GCF_000242255.2_ASM24225v3_genomic.fna.gz | prodigal -d GCF_000242255.2_ASM24225v3_genomic.fna/cds.fna -a GCF_000242255.2_ASM24225v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:23,471] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:23,472] [INFO] Task started: HMMsearch
[2024-01-24 13:01:23,472] [INFO] Running command: hmmsearch --tblout GCF_000242255.2_ASM24225v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference/reference_markers.hmm GCF_000242255.2_ASM24225v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:23,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:23,730] [INFO] Found 6/6 markers.
[2024-01-24 13:01:23,769] [INFO] Query marker FASTA was written to GCF_000242255.2_ASM24225v3_genomic.fna/markers.fasta
[2024-01-24 13:01:23,770] [INFO] Task started: Blastn
[2024-01-24 13:01:23,770] [INFO] Running command: blastn -query GCF_000242255.2_ASM24225v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference/reference_markers.fasta -out GCF_000242255.2_ASM24225v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:24,699] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:24,711] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:24,712] [INFO] Target genome list was writen to GCF_000242255.2_ASM24225v3_genomic.fna/target_genomes.txt
[2024-01-24 13:01:24,718] [INFO] Task started: fastANI
[2024-01-24 13:01:24,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg9435cea5-fb10-4711-be46-0e81a7033b98/GCF_000242255.2_ASM24225v3_genomic.fna.gz --refList GCF_000242255.2_ASM24225v3_genomic.fna/target_genomes.txt --output GCF_000242255.2_ASM24225v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:37,143] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:37,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:37,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:37,160] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:37,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:37,161] [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
Frateuria aurantia	strain=DSM 6220	GCA_000242255.3	81475	81475	type	True	100.0	1199	1201	95	conclusive
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	78.7415	304	1201	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	78.6867	256	1201	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	78.5942	326	1201	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	78.5567	317	1201	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	78.518	299	1201	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	78.4865	336	1201	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.4661	287	1201	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	78.4111	297	1201	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.4002	338	1201	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	78.2652	296	1201	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.1875	340	1201	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	78.0409	310	1201	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	77.2406	218	1201	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	77.1738	171	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:37,163] [INFO] DFAST Taxonomy check result was written to GCF_000242255.2_ASM24225v3_genomic.fna/tc_result.tsv
[2024-01-24 13:01:37,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:37,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:37,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference/checkm_data
[2024-01-24 13:01:37,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:37,203] [INFO] Task started: CheckM
[2024-01-24 13:01:37,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000242255.2_ASM24225v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000242255.2_ASM24225v3_genomic.fna/checkm_input GCF_000242255.2_ASM24225v3_genomic.fna/checkm_result
[2024-01-24 13:02:27,268] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:27,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:27,289] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:27,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:27,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000242255.2_ASM24225v3_genomic.fna/markers.fasta)
[2024-01-24 13:02:27,289] [INFO] Task started: Blastn
[2024-01-24 13:02:27,290] [INFO] Running command: blastn -query GCF_000242255.2_ASM24225v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg640d996f-5869-4adb-b454-29ddf5804aad/dqc_reference/reference_markers_gtdb.fasta -out GCF_000242255.2_ASM24225v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:28,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:28,885] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:28,885] [INFO] Target genome list was writen to GCF_000242255.2_ASM24225v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:28,917] [INFO] Task started: fastANI
[2024-01-24 13:02:28,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg9435cea5-fb10-4711-be46-0e81a7033b98/GCF_000242255.2_ASM24225v3_genomic.fna.gz --refList GCF_000242255.2_ASM24225v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000242255.2_ASM24225v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:43,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:43,216] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:43,216] [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_000242255.2	s__Frateuria aurantia	100.0	1200	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003201105.1	s__Dyella jiangningensis_B	78.7961	332	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900112865.1	s__Dyella marensis	78.6819	358	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003332825.1	s__Dyella sp003332825	78.5459	345	1201	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	78.5101	335	1201	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	78.5055	317	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	78.4998	378	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_001182895.1	s__Frateuria_B defendens	78.4849	357	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438785.1	s__Rhodanobacter glycinis_A	78.4373	307	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.18	99.18	0.94	0.94	2	-
GCF_016586165.1	s__Dyella sp016586165	78.4234	313	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115705.1	s__Frateuria_A terrea	78.4158	297	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002279065.1	s__Dyella_A sp002279065	78.4044	319	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_000632805.1	s__Dyella jiangningensis	78.3777	328	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842975.1	s__Rhodanobacter sp014842975	78.3104	334	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001175.1	s__Rhodanobacter sp002001175	78.3014	299	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114495.1	s__Dyella sp900114495	78.2928	278	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	78.2076	241	1201	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_001617365.1	s__Rhodanobacter sp001617365	78.1689	332	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_000264315.1	s__Rhodanobacter fulvus	78.0629	308	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:43,219] [INFO] GTDB search result was written to GCF_000242255.2_ASM24225v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:43,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:43,225] [INFO] DFAST_QC result json was written to GCF_000242255.2_ASM24225v3_genomic.fna/dqc_result.json
[2024-01-24 13:02:43,226] [INFO] DFAST_QC completed!
[2024-01-24 13:02:43,226] [INFO] Total running time: 0h1m33s