[2023-06-27 19:44:53,110] [INFO] DFAST_QC pipeline started.
[2023-06-27 19:44:53,113] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 19:44:53,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference
[2023-06-27 19:44:54,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 19:44:54,682] [INFO] Task started: Prodigal
[2023-06-27 19:44:54,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg90943fd1-de05-4ac6-acbf-3185eb2ad2a2/GCA_027489775.1_ASM2748977v1_genomic.fna.gz | prodigal -d GCA_027489775.1_ASM2748977v1_genomic.fna/cds.fna -a GCA_027489775.1_ASM2748977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 19:45:01,916] [INFO] Task succeeded: Prodigal
[2023-06-27 19:45:01,916] [INFO] Task started: HMMsearch
[2023-06-27 19:45:01,917] [INFO] Running command: hmmsearch --tblout GCA_027489775.1_ASM2748977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference/reference_markers.hmm GCA_027489775.1_ASM2748977v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 19:45:02,173] [INFO] Task succeeded: HMMsearch
[2023-06-27 19:45:02,174] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90943fd1-de05-4ac6-acbf-3185eb2ad2a2/GCA_027489775.1_ASM2748977v1_genomic.fna.gz]
[2023-06-27 19:45:02,211] [INFO] Query marker FASTA was written to GCA_027489775.1_ASM2748977v1_genomic.fna/markers.fasta
[2023-06-27 19:45:02,211] [INFO] Task started: Blastn
[2023-06-27 19:45:02,211] [INFO] Running command: blastn -query GCA_027489775.1_ASM2748977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference/reference_markers.fasta -out GCA_027489775.1_ASM2748977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:45:03,023] [INFO] Task succeeded: Blastn
[2023-06-27 19:45:03,026] [INFO] Selected 30 target genomes.
[2023-06-27 19:45:03,027] [INFO] Target genome list was writen to GCA_027489775.1_ASM2748977v1_genomic.fna/target_genomes.txt
[2023-06-27 19:45:03,032] [INFO] Task started: fastANI
[2023-06-27 19:45:03,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg90943fd1-de05-4ac6-acbf-3185eb2ad2a2/GCA_027489775.1_ASM2748977v1_genomic.fna.gz --refList GCA_027489775.1_ASM2748977v1_genomic.fna/target_genomes.txt --output GCA_027489775.1_ASM2748977v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 19:45:25,115] [INFO] Task succeeded: fastANI
[2023-06-27 19:45:25,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 19:45:25,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 19:45:25,137] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 19:45:25,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 19:45:25,138] [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
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.9731	140	710	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.9387	127	710	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.7088	133	710	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.7025	118	710	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	76.6889	168	710	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	76.593	130	710	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	76.5447	75	710	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	76.5421	107	710	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.4697	136	710	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.4664	109	710	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.4576	105	710	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	76.4422	87	710	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.4222	116	710	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	76.377	84	710	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	76.3736	105	710	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	76.3548	97	710	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	76.3426	84	710	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.3236	80	710	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	76.3172	117	710	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.2833	109	710	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.2771	109	710	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.2121	80	710	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.2006	139	710	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	76.1886	54	710	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	76.188	111	710	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	76.0985	80	710	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	76.0802	85	710	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.0132	77	710	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	75.9848	98	710	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	75.8501	64	710	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 19:45:25,141] [INFO] DFAST Taxonomy check result was written to GCA_027489775.1_ASM2748977v1_genomic.fna/tc_result.tsv
[2023-06-27 19:45:25,141] [INFO] ===== Taxonomy check completed =====
[2023-06-27 19:45:25,142] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 19:45:25,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference/checkm_data
[2023-06-27 19:45:25,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 19:45:25,176] [INFO] Task started: CheckM
[2023-06-27 19:45:25,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027489775.1_ASM2748977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027489775.1_ASM2748977v1_genomic.fna/checkm_input GCA_027489775.1_ASM2748977v1_genomic.fna/checkm_result
[2023-06-27 19:45:52,289] [INFO] Task succeeded: CheckM
[2023-06-27 19:45:52,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 19:45:52,319] [INFO] ===== Completeness check finished =====
[2023-06-27 19:45:52,320] [INFO] ===== Start GTDB Search =====
[2023-06-27 19:45:52,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027489775.1_ASM2748977v1_genomic.fna/markers.fasta)
[2023-06-27 19:45:52,320] [INFO] Task started: Blastn
[2023-06-27 19:45:52,321] [INFO] Running command: blastn -query GCA_027489775.1_ASM2748977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357a10c0-967a-4b4b-866b-f35b569ede48/dqc_reference/reference_markers_gtdb.fasta -out GCA_027489775.1_ASM2748977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:45:53,740] [INFO] Task succeeded: Blastn
[2023-06-27 19:45:53,744] [INFO] Selected 29 target genomes.
[2023-06-27 19:45:53,744] [INFO] Target genome list was writen to GCA_027489775.1_ASM2748977v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 19:45:53,774] [INFO] Task started: fastANI
[2023-06-27 19:45:53,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg90943fd1-de05-4ac6-acbf-3185eb2ad2a2/GCA_027489775.1_ASM2748977v1_genomic.fna.gz --refList GCA_027489775.1_ASM2748977v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027489775.1_ASM2748977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 19:46:12,948] [INFO] Task succeeded: fastANI
[2023-06-27 19:46:12,973] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 19:46:12,974] [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_903837135.1	s__CAIOYC01 sp903837135	77.0513	155	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.97	99.97	0.97	0.97	3	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	77.0507	114	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001794825.1	s__Brevundimonas sp001794825	76.9548	128	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696695.1	s__Terricaulis sp900696695	76.9243	125	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	99.53	99.53	0.91	0.91	2	-
GCA_018241995.1	s__17J80-11 sp018241995	76.8915	126	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280485.1	s__NCED01 sp002280485	76.8115	120	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__NCED01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969015.1	s__REEB506 sp018969015	76.7873	153	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__REEB506	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714495.1	s__UBA7672 sp016714495	76.6878	73	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302105.1	s__Brevundimonas sp017302105	76.6237	75	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123845.1	s__Bosea sp004123845	76.6182	110	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196335.1	s__Brevundimonas lenta	76.593	130	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234965.1	s__Aestuariivirga litoralis	76.5421	107	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793285.1	s__Phenylobacterium sp016793285	76.5107	153	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	76.4845	108	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793225.1	s__Phenylobacterium sp016793225	76.4811	144	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907975.1	s__Methylopila capsulata	76.445	100	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	76.377	84	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_000702305.1	s__GCF-000702305 sp000702305	76.3462	109	710	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_014636935.1	s__Alsobacter metallidurans	76.3155	99	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341515.1	s__Bosea sp004341515	76.2681	115	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748145.1	s__Bosea sp001748145	76.2171	103	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	76.1886	54	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191355.1	s__Methylobacterium sp014191355	76.1549	94	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	76.1533	109	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCA_016869215.1	s__Z2-YC6860 sp016869215	76.1194	94	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	76.1076	68	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	76.0528	92	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137085.1	s__Lichenihabitans ramalinae	75.9848	98	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296935.1	s__Reyranella sp004296935	75.9649	80	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 19:46:12,976] [INFO] GTDB search result was written to GCA_027489775.1_ASM2748977v1_genomic.fna/result_gtdb.tsv
[2023-06-27 19:46:12,977] [INFO] ===== GTDB Search completed =====
[2023-06-27 19:46:12,983] [INFO] DFAST_QC result json was written to GCA_027489775.1_ASM2748977v1_genomic.fna/dqc_result.json
[2023-06-27 19:46:12,983] [INFO] DFAST_QC completed!
[2023-06-27 19:46:12,984] [INFO] Total running time: 0h1m20s