[2023-06-29 03:06:27,156] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:06:27,161] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:06:27,161] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference
[2023-06-29 03:06:28,495] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:06:28,496] [INFO] Task started: Prodigal
[2023-06-29 03:06:28,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ac0fef5-48c5-463e-b5a9-3a4e91f70a08/GCA_020849325.1_ASM2084932v1_genomic.fna.gz | prodigal -d GCA_020849325.1_ASM2084932v1_genomic.fna/cds.fna -a GCA_020849325.1_ASM2084932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:06:35,715] [INFO] Task succeeded: Prodigal
[2023-06-29 03:06:35,715] [INFO] Task started: HMMsearch
[2023-06-29 03:06:35,716] [INFO] Running command: hmmsearch --tblout GCA_020849325.1_ASM2084932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference/reference_markers.hmm GCA_020849325.1_ASM2084932v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:06:35,988] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:06:35,989] [INFO] Found 6/6 markers.
[2023-06-29 03:06:36,038] [INFO] Query marker FASTA was written to GCA_020849325.1_ASM2084932v1_genomic.fna/markers.fasta
[2023-06-29 03:06:36,039] [INFO] Task started: Blastn
[2023-06-29 03:06:36,039] [INFO] Running command: blastn -query GCA_020849325.1_ASM2084932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference/reference_markers.fasta -out GCA_020849325.1_ASM2084932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:06:37,171] [INFO] Task succeeded: Blastn
[2023-06-29 03:06:37,174] [INFO] Selected 19 target genomes.
[2023-06-29 03:06:37,175] [INFO] Target genome list was writen to GCA_020849325.1_ASM2084932v1_genomic.fna/target_genomes.txt
[2023-06-29 03:06:37,176] [INFO] Task started: fastANI
[2023-06-29 03:06:37,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ac0fef5-48c5-463e-b5a9-3a4e91f70a08/GCA_020849325.1_ASM2084932v1_genomic.fna.gz --refList GCA_020849325.1_ASM2084932v1_genomic.fna/target_genomes.txt --output GCA_020849325.1_ASM2084932v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:06:54,458] [INFO] Task succeeded: fastANI
[2023-06-29 03:06:54,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:06:54,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:06:54,475] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:06:54,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:06:54,476] [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
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.7161	308	922	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.6351	297	922	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.5569	266	922	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.4863	277	922	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.4063	351	922	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	77.3602	236	922	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	77.3568	217	922	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.1753	277	922	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.1307	238	922	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	77.1213	251	922	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.0928	248	922	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	77.0928	203	922	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.0487	256	922	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.0462	277	922	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.967	272	922	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	76.861	213	922	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.8557	246	922	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.7125	299	922	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.6957	304	922	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:06:54,478] [INFO] DFAST Taxonomy check result was written to GCA_020849325.1_ASM2084932v1_genomic.fna/tc_result.tsv
[2023-06-29 03:06:54,478] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:06:54,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:06:54,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference/checkm_data
[2023-06-29 03:06:54,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:06:54,516] [INFO] Task started: CheckM
[2023-06-29 03:06:54,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020849325.1_ASM2084932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020849325.1_ASM2084932v1_genomic.fna/checkm_input GCA_020849325.1_ASM2084932v1_genomic.fna/checkm_result
[2023-06-29 03:07:21,143] [INFO] Task succeeded: CheckM
[2023-06-29 03:07:21,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:07:21,171] [INFO] ===== Completeness check finished =====
[2023-06-29 03:07:21,171] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:07:21,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020849325.1_ASM2084932v1_genomic.fna/markers.fasta)
[2023-06-29 03:07:21,172] [INFO] Task started: Blastn
[2023-06-29 03:07:21,172] [INFO] Running command: blastn -query GCA_020849325.1_ASM2084932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dd1da4c-c550-459a-8eaa-2d2d2e70f006/dqc_reference/reference_markers_gtdb.fasta -out GCA_020849325.1_ASM2084932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:07:23,412] [INFO] Task succeeded: Blastn
[2023-06-29 03:07:23,416] [INFO] Selected 22 target genomes.
[2023-06-29 03:07:23,416] [INFO] Target genome list was writen to GCA_020849325.1_ASM2084932v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:07:23,425] [INFO] Task started: fastANI
[2023-06-29 03:07:23,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ac0fef5-48c5-463e-b5a9-3a4e91f70a08/GCA_020849325.1_ASM2084932v1_genomic.fna.gz --refList GCA_020849325.1_ASM2084932v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020849325.1_ASM2084932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:07:41,111] [INFO] Task succeeded: fastANI
[2023-06-29 03:07:41,141] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:07:41,141] [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_017305635.1	s__Bauldia sp017305635	78.0866	321	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	77.9928	336	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	77.7571	304	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	77.7495	306	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	77.6556	315	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	77.6075	224	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	77.5346	268	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_000380505.1	s__Kaistia granuli	77.4857	278	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.4487	280	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	77.4239	348	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000496075.1	s__Lutibaculum baratangense	77.3825	234	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711085.1	s__JADJTR01 sp016711085	77.3766	178	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JADJTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	77.3449	217	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	77.2601	252	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.1958	274	922	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_001305515.1	s__Prosthecomicrobium_A hirschii	77.1912	306	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCA_900466745.1	s__Bosea sp900466745	77.173	270	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCA_017305925.1	s__JAFKJW01 sp017305925	77.144	212	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294985.1	s__Mesorhizobium sp002294985	77.1309	215	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	-
GCA_013377085.1	s__Rhodoplanes sp013377085	76.9202	285	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004555.2	s__Methylobacterium sp004004555	76.7198	298	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	76.5385	198	922	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:07:41,143] [INFO] GTDB search result was written to GCA_020849325.1_ASM2084932v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:07:41,144] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:07:41,148] [INFO] DFAST_QC result json was written to GCA_020849325.1_ASM2084932v1_genomic.fna/dqc_result.json
[2023-06-29 03:07:41,149] [INFO] DFAST_QC completed!
[2023-06-29 03:07:41,149] [INFO] Total running time: 0h1m14s