[2024-01-24 13:18:46,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference
[2024-01-24 13:18:47,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,726] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg681aaa68-24a1-4dc7-bd78-007c99f67ddd/GCF_013376135.1_ASM1337613v1_genomic.fna.gz | prodigal -d GCF_013376135.1_ASM1337613v1_genomic.fna/cds.fna -a GCF_013376135.1_ASM1337613v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:56,014] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:56,014] [INFO] Task started: HMMsearch
[2024-01-24 13:18:56,014] [INFO] Running command: hmmsearch --tblout GCF_013376135.1_ASM1337613v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference/reference_markers.hmm GCF_013376135.1_ASM1337613v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:56,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:56,279] [INFO] Found 6/6 markers.
[2024-01-24 13:18:56,325] [INFO] Query marker FASTA was written to GCF_013376135.1_ASM1337613v1_genomic.fna/markers.fasta
[2024-01-24 13:18:56,325] [INFO] Task started: Blastn
[2024-01-24 13:18:56,325] [INFO] Running command: blastn -query GCF_013376135.1_ASM1337613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference/reference_markers.fasta -out GCF_013376135.1_ASM1337613v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:57,330] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:57,333] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:57,333] [INFO] Target genome list was writen to GCF_013376135.1_ASM1337613v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:57,349] [INFO] Task started: fastANI
[2024-01-24 13:18:57,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg681aaa68-24a1-4dc7-bd78-007c99f67ddd/GCF_013376135.1_ASM1337613v1_genomic.fna.gz --refList GCF_013376135.1_ASM1337613v1_genomic.fna/target_genomes.txt --output GCF_013376135.1_ASM1337613v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:13,313] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:13,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:13,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:13,331] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:13,331] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:13,332] [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
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	100.0	704	717	95	conclusive
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	99.9874	710	717	95	conclusive
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.5658	154	717	95	below_threshold
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	78.4968	126	717	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	78.4952	214	717	95	below_threshold
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	78.4875	121	717	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.3459	219	717	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.3239	207	717	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.3212	224	717	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	78.2903	228	717	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	78.0578	238	717	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.9513	192	717	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	77.6305	188	717	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	77.5124	191	717	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.299	117	717	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	77.2525	138	717	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	77.1621	175	717	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	77.1394	157	717	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.9007	127	717	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.5219	153	717	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.4098	141	717	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.2976	127	717	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.2969	90	717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:13,333] [INFO] DFAST Taxonomy check result was written to GCF_013376135.1_ASM1337613v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:13,334] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:13,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:13,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference/checkm_data
[2024-01-24 13:19:13,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:13,372] [INFO] Task started: CheckM
[2024-01-24 13:19:13,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013376135.1_ASM1337613v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013376135.1_ASM1337613v1_genomic.fna/checkm_input GCF_013376135.1_ASM1337613v1_genomic.fna/checkm_result
[2024-01-24 13:19:41,667] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:41,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:41,687] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:41,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:41,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013376135.1_ASM1337613v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:41,688] [INFO] Task started: Blastn
[2024-01-24 13:19:41,688] [INFO] Running command: blastn -query GCF_013376135.1_ASM1337613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bab026a-5830-4bda-8ecd-2376786f0239/dqc_reference/reference_markers_gtdb.fasta -out GCF_013376135.1_ASM1337613v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:43,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:43,345] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:43,346] [INFO] Target genome list was writen to GCF_013376135.1_ASM1337613v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:43,378] [INFO] Task started: fastANI
[2024-01-24 13:19:43,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg681aaa68-24a1-4dc7-bd78-007c99f67ddd/GCF_013376135.1_ASM1337613v1_genomic.fna.gz --refList GCF_013376135.1_ASM1337613v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013376135.1_ASM1337613v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:58,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,958] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:58,959] [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_014192375.1	s__Endobacter medicaginis	99.9874	710	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Endobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_903844135.1	s__Lichenicola sp903844135	79.5135	301	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.79	99.79	0.94	0.94	2	-
GCF_005844085.1	s__Lichenicoccus roseus	79.2855	284	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	78.5392	155	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	78.4052	225	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	78.3965	158	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201075.1	s__Lichenicola cladoniae	78.3874	276	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	78.3722	199	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.338	223	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCA_903907955.1	s__BOG-930 sp903907955	78.296	186	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCF_008630155.1	s__Rhodovastum atsumiense	78.0929	237	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	78.0695	235	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCF_000164635.1	s__Roseomonas cervicalis	77.9524	192	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906255.1	s__Komagataeibacter maltaceti	77.8792	154	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.6676	200	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	77.6565	238	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	77.5752	186	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_004761865.1	s__Crenalkalicoccus roseus	77.5161	208	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924855.1	s__CAIQQQ01 sp903924855	77.2882	146	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIQQQ01	95.0	99.77	99.77	0.89	0.89	2	-
GCA_903944925.1	s__Rhodopila sp903944925	77.2593	152	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
GCA_903915725.1	s__Rhodopila sp903915725	76.8036	153	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	100.00	100.00	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,961] [INFO] GTDB search result was written to GCF_013376135.1_ASM1337613v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:58,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:58,966] [INFO] DFAST_QC result json was written to GCF_013376135.1_ASM1337613v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:58,966] [INFO] DFAST_QC completed!
[2024-01-24 13:19:58,966] [INFO] Total running time: 0h1m13s