[2024-01-24 15:03:29,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,831] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference
[2024-01-24 15:03:31,224] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:31,225] [INFO] Task started: Prodigal
[2024-01-24 15:03:31,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e92f161-e965-4f9c-8a61-1b8a0c8a4e61/GCF_025994335.1_ASM2599433v1_genomic.fna.gz | prodigal -d GCF_025994335.1_ASM2599433v1_genomic.fna/cds.fna -a GCF_025994335.1_ASM2599433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:42,483] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:42,484] [INFO] Task started: HMMsearch
[2024-01-24 15:03:42,484] [INFO] Running command: hmmsearch --tblout GCF_025994335.1_ASM2599433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference/reference_markers.hmm GCF_025994335.1_ASM2599433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:42,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:42,754] [INFO] Found 6/6 markers.
[2024-01-24 15:03:42,793] [INFO] Query marker FASTA was written to GCF_025994335.1_ASM2599433v1_genomic.fna/markers.fasta
[2024-01-24 15:03:42,794] [INFO] Task started: Blastn
[2024-01-24 15:03:42,794] [INFO] Running command: blastn -query GCF_025994335.1_ASM2599433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference/reference_markers.fasta -out GCF_025994335.1_ASM2599433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:43,749] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:43,752] [INFO] Selected 23 target genomes.
[2024-01-24 15:03:43,752] [INFO] Target genome list was writen to GCF_025994335.1_ASM2599433v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:43,761] [INFO] Task started: fastANI
[2024-01-24 15:03:43,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e92f161-e965-4f9c-8a61-1b8a0c8a4e61/GCF_025994335.1_ASM2599433v1_genomic.fna.gz --refList GCF_025994335.1_ASM2599433v1_genomic.fna/target_genomes.txt --output GCF_025994335.1_ASM2599433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:00,850] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:00,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:00,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:00,876] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:04:00,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:04:00,876] [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
Tanticharoenia sakaeratensis	strain=NBRC 103193	GCA_000963885.1	444053	444053	type	True	99.9914	1113	1136	95	conclusive
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_002005465.1	320497	320497	type	True	79.0889	297	1136	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_007991115.1	320497	320497	type	True	78.8151	289	1136	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	78.3019	281	1136	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	78.2403	276	1136	95	below_threshold
Acidomonas methanolica	strain=DSM 5432	GCA_004346035.1	437	437	type	True	78.2189	290	1136	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.2023	274	1136	95	below_threshold
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	78.1957	284	1136	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.1099	277	1136	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	77.8562	176	1136	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.8428	170	1136	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	77.8112	255	1136	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	77.7222	181	1136	95	below_threshold
Gluconobacter kanchanaburiensis	strain=NBRC 103587	GCA_007988905.1	563199	563199	type	True	77.5209	153	1136	95	below_threshold
Granulibacter bethesdensis	strain=CGDNIH1	GCA_000014285.2	364410	364410	type	True	76.8291	77	1136	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.3588	87	1136	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.3524	122	1136	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.2174	59	1136	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.1109	60	1136	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.9976	87	1136	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.6785	100	1136	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.6521	70	1136	95	below_threshold
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	75.6484	67	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:00,878] [INFO] DFAST Taxonomy check result was written to GCF_025994335.1_ASM2599433v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:00,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:00,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:00,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference/checkm_data
[2024-01-24 15:04:00,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:00,918] [INFO] Task started: CheckM
[2024-01-24 15:04:00,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994335.1_ASM2599433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994335.1_ASM2599433v1_genomic.fna/checkm_input GCF_025994335.1_ASM2599433v1_genomic.fna/checkm_result
[2024-01-24 15:04:38,621] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:38,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:38,642] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:38,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:38,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994335.1_ASM2599433v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:38,644] [INFO] Task started: Blastn
[2024-01-24 15:04:38,644] [INFO] Running command: blastn -query GCF_025994335.1_ASM2599433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0e775cd-559b-49e2-ad71-f8e1105f4433/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994335.1_ASM2599433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:40,511] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:40,514] [INFO] Selected 19 target genomes.
[2024-01-24 15:04:40,514] [INFO] Target genome list was writen to GCF_025994335.1_ASM2599433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:40,529] [INFO] Task started: fastANI
[2024-01-24 15:04:40,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e92f161-e965-4f9c-8a61-1b8a0c8a4e61/GCF_025994335.1_ASM2599433v1_genomic.fna.gz --refList GCF_025994335.1_ASM2599433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994335.1_ASM2599433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:53,728] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:53,742] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:53,742] [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_000963885.1	s__Tanticharoenia sakaeratensis	99.9914	1113	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Tanticharoenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002005465.1	s__Neoasaia chiangmaiensis	79.0889	297	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013376175.1	s__Ameyamaea chiangmaiensis	78.5071	214	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004346035.1	s__Acidomonas methanolica	78.2343	287	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_018811945.1	s__Gluconobacter sp018811945	78.1792	212	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.1099	277	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174255.1	s__Gluconacetobacter sacchari	77.922	249	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	77.8899	273	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547995.1	s__Asaia bogorensis	77.862	175	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_014174375.1	s__Gluconacetobacter asukensis	77.8532	254	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.8285	170	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	77.7979	256	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_018256155.1	s__Gluconobacter sp018256155	77.7611	212	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	77.6797	258	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	77.6434	266	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_005844085.1	s__Lichenicoccus roseus	77.2532	226	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014285.2	s__Granulibacter bethesdensis	76.829	76	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Granulibacter	95.0	98.35	95.29	0.97	0.95	8	-
GCA_903881515.1	s__CAIRTN01 sp903881515	76.3337	100	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIRTN01	95.0	99.60	99.60	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:53,744] [INFO] GTDB search result was written to GCF_025994335.1_ASM2599433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:53,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:53,749] [INFO] DFAST_QC result json was written to GCF_025994335.1_ASM2599433v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:53,749] [INFO] DFAST_QC completed!
[2024-01-24 15:04:53,749] [INFO] Total running time: 0h1m24s