[2024-01-25 18:47:20,789] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:20,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:20,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference
[2024-01-25 18:47:21,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:21,913] [INFO] Task started: Prodigal
[2024-01-25 18:47:21,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg63d438fd-7f00-4e7b-99fd-d12879c660f9/GCF_014635245.1_ASM1463524v1_genomic.fna.gz | prodigal -d GCF_014635245.1_ASM1463524v1_genomic.fna/cds.fna -a GCF_014635245.1_ASM1463524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:32,120] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:32,120] [INFO] Task started: HMMsearch
[2024-01-25 18:47:32,120] [INFO] Running command: hmmsearch --tblout GCF_014635245.1_ASM1463524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference/reference_markers.hmm GCF_014635245.1_ASM1463524v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:32,337] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:32,338] [INFO] Found 6/6 markers.
[2024-01-25 18:47:32,370] [INFO] Query marker FASTA was written to GCF_014635245.1_ASM1463524v1_genomic.fna/markers.fasta
[2024-01-25 18:47:32,370] [INFO] Task started: Blastn
[2024-01-25 18:47:32,370] [INFO] Running command: blastn -query GCF_014635245.1_ASM1463524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference/reference_markers.fasta -out GCF_014635245.1_ASM1463524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:33,260] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:33,263] [INFO] Selected 29 target genomes.
[2024-01-25 18:47:33,263] [INFO] Target genome list was writen to GCF_014635245.1_ASM1463524v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:33,292] [INFO] Task started: fastANI
[2024-01-25 18:47:33,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg63d438fd-7f00-4e7b-99fd-d12879c660f9/GCF_014635245.1_ASM1463524v1_genomic.fna.gz --refList GCF_014635245.1_ASM1463524v1_genomic.fna/target_genomes.txt --output GCF_014635245.1_ASM1463524v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:58,136] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:58,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:58,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:58,153] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:58,153] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:58,153] [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
Agaricicola taiwanensis	strain=CCM 7684	GCA_014635245.1	591372	591372	type	True	100.0	1245	1245	95	conclusive
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.7152	295	1245	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.6838	235	1245	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	77.3898	221	1245	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.3856	218	1245	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.3351	255	1245	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.3073	224	1245	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.2591	255	1245	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	77.248	206	1245	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	77.2212	183	1245	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	77.2148	183	1245	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	77.1989	244	1245	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.148	201	1245	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	77.1365	193	1245	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	77.1334	172	1245	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.0874	212	1245	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.0677	219	1245	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	77.0247	178	1245	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.0194	218	1245	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	76.9944	211	1245	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	76.9475	172	1245	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.9277	214	1245	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.9166	207	1245	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	76.8683	166	1245	95	below_threshold
Methylobacterium marchantiae	strain=DSM 21328	GCA_022179405.1	600331	600331	type	True	76.826	166	1245	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.7732	221	1245	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	76.7399	218	1245	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.7385	207	1245	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.7216	206	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:58,154] [INFO] DFAST Taxonomy check result was written to GCF_014635245.1_ASM1463524v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:58,156] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:58,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:58,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference/checkm_data
[2024-01-25 18:47:58,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:58,194] [INFO] Task started: CheckM
[2024-01-25 18:47:58,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635245.1_ASM1463524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635245.1_ASM1463524v1_genomic.fna/checkm_input GCF_014635245.1_ASM1463524v1_genomic.fna/checkm_result
[2024-01-25 18:48:31,537] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:31,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:31,559] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:31,559] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:31,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635245.1_ASM1463524v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:31,560] [INFO] Task started: Blastn
[2024-01-25 18:48:31,561] [INFO] Running command: blastn -query GCF_014635245.1_ASM1463524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39c26f50-27f3-4c1b-8d97-27a4882936a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635245.1_ASM1463524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:33,276] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:33,281] [INFO] Selected 29 target genomes.
[2024-01-25 18:48:33,281] [INFO] Target genome list was writen to GCF_014635245.1_ASM1463524v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:33,323] [INFO] Task started: fastANI
[2024-01-25 18:48:33,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg63d438fd-7f00-4e7b-99fd-d12879c660f9/GCF_014635245.1_ASM1463524v1_genomic.fna.gz --refList GCF_014635245.1_ASM1463524v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635245.1_ASM1463524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:56,085] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:56,102] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:56,102] [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_014635245.1	s__Agaricicola taiwanensis	100.0	1245	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Agaricicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014196925.1	s__Chelatococcus_A caeni	77.7227	295	1245	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_000010525.1	s__Azorhizobium caulinodans	77.6836	235	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCA_014191545.1	s__Ga0077545 sp014191545	77.4737	181	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347645.1	s__Ga0077545 sp003347645	77.4368	218	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897035.1	s__Methylopila sp002897035	77.409	223	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	77.4032	220	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398315.1	s__Chelatococcus sp018398315	77.3827	181	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390695.1	s__Ancylobacter_B sonchi	77.3351	255	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297465.1	s__SCUB01 sp004297465	77.2945	193	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__SCUB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	77.2593	218	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	77.237	257	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	77.2333	235	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	77.2254	243	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402875.1	s__Blastochloris viridis	77.2148	183	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	77.1718	223	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713455.1	s__Bosea sp001713455	77.1672	248	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	77.1535	175	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCA_001464335.1	s__Ga0077545 sp001464335	77.1415	185	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839445.1	s__Chthonobacter albigriseus	77.1365	193	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517025.1	s__Pinisolibacter sp012517025	77.0857	158	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.0748	213	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	77.0071	214	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636935.1	s__Alsobacter metallidurans	76.9327	215	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	76.8645	130	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899525.1	s__65-9 sp001899525	76.8457	177	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__65-9	95.0	99.88	99.88	0.96	0.96	2	-
GCF_000426105.1	s__Bradyrhizobium sp000426105	76.8281	165	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	76.7717	221	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	76.7293	219	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:56,103] [INFO] GTDB search result was written to GCF_014635245.1_ASM1463524v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:56,104] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:56,109] [INFO] DFAST_QC result json was written to GCF_014635245.1_ASM1463524v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:56,109] [INFO] DFAST_QC completed!
[2024-01-25 18:48:56,109] [INFO] Total running time: 0h1m35s