[2024-01-24 14:30:46,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:46,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:46,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference
[2024-01-24 14:30:48,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,092] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg32c9464b-8d9a-4a1d-8cb6-b04f8b67516e/GCF_014197015.1_ASM1419701v1_genomic.fna.gz | prodigal -d GCF_014197015.1_ASM1419701v1_genomic.fna/cds.fna -a GCF_014197015.1_ASM1419701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:03,698] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:03,698] [INFO] Task started: HMMsearch
[2024-01-24 14:31:03,698] [INFO] Running command: hmmsearch --tblout GCF_014197015.1_ASM1419701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference/reference_markers.hmm GCF_014197015.1_ASM1419701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:04,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:04,027] [INFO] Found 6/6 markers.
[2024-01-24 14:31:04,065] [INFO] Query marker FASTA was written to GCF_014197015.1_ASM1419701v1_genomic.fna/markers.fasta
[2024-01-24 14:31:04,066] [INFO] Task started: Blastn
[2024-01-24 14:31:04,066] [INFO] Running command: blastn -query GCF_014197015.1_ASM1419701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference/reference_markers.fasta -out GCF_014197015.1_ASM1419701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:05,028] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:05,031] [INFO] Selected 19 target genomes.
[2024-01-24 14:31:05,032] [INFO] Target genome list was writen to GCF_014197015.1_ASM1419701v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:05,041] [INFO] Task started: fastANI
[2024-01-24 14:31:05,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c9464b-8d9a-4a1d-8cb6-b04f8b67516e/GCF_014197015.1_ASM1419701v1_genomic.fna.gz --refList GCF_014197015.1_ASM1419701v1_genomic.fna/target_genomes.txt --output GCF_014197015.1_ASM1419701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:23,344] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:23,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:23,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:23,362] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:23,363] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:23,363] [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
Niveibacterium umoris	strain=DSM 106739	GCA_014197015.1	1193620	1193620	type	True	100.0	1591	1593	95	conclusive
Niveibacterium umoris	strain=KACC 17062	GCA_017311475.1	1193620	1193620	type	True	99.9853	1568	1593	95	conclusive
Niveibacterium microcysteis	strain=HC41	GCA_017161445.1	2811415	2811415	type	True	84.8318	1049	1593	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.7051	348	1593	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	78.57	341	1593	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	78.5316	310	1593	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	78.2348	344	1593	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.1766	280	1593	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.0894	345	1593	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.0823	350	1593	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.0288	381	1593	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	77.9522	361	1593	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	77.774	353	1593	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.6567	320	1593	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	77.6148	233	1593	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.0252	238	1593	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7828	320	1593	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.3849	134	1593	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.3106	141	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:23,365] [INFO] DFAST Taxonomy check result was written to GCF_014197015.1_ASM1419701v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:23,366] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:23,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:23,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference/checkm_data
[2024-01-24 14:31:23,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:23,419] [INFO] Task started: CheckM
[2024-01-24 14:31:23,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197015.1_ASM1419701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197015.1_ASM1419701v1_genomic.fna/checkm_input GCF_014197015.1_ASM1419701v1_genomic.fna/checkm_result
[2024-01-24 14:32:19,963] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:19,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:19,981] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:19,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:19,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197015.1_ASM1419701v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:19,982] [INFO] Task started: Blastn
[2024-01-24 14:32:19,982] [INFO] Running command: blastn -query GCF_014197015.1_ASM1419701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e249b39-d013-43d2-84ff-d8c4a1fb5b81/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197015.1_ASM1419701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:21,839] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:21,842] [INFO] Selected 20 target genomes.
[2024-01-24 14:32:21,843] [INFO] Target genome list was writen to GCF_014197015.1_ASM1419701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:21,858] [INFO] Task started: fastANI
[2024-01-24 14:32:21,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c9464b-8d9a-4a1d-8cb6-b04f8b67516e/GCF_014197015.1_ASM1419701v1_genomic.fna.gz --refList GCF_014197015.1_ASM1419701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197015.1_ASM1419701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:38,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:38,160] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:38,161] [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_014197015.1	s__Niveibacterium umoris	100.0	1591	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017161445.1	s__Niveibacterium microcysteis	84.8519	1050	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	97.91	97.91	0.91	0.91	2	-
GCF_001591165.1	s__Thauera butanivorans	78.7284	346	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	78.6072	339	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_002245655.1	s__Thauera propionica	78.5925	339	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCF_001696715.1	s__Thauera phenolivorans	78.5549	308	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_001682385.1	s__Azoarcus olearius	78.2588	386	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	-
GCF_006539865.1	s__Zoogloea ramigera	78.2216	345	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	99.03	99.03	0.93	0.93	2	-
GCA_017302295.1	s__Thauera sp017302295	78.1347	326	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910785.1	s__Aromatoleum buckelii	78.1309	290	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	78.1116	343	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018240585.1	s__Thauera sp018240585	78.0813	302	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781175.1	s__Niveibacterium sp009781175	78.0686	290	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014736495.1	s__Dactylopiibacterium carminicum	78.0429	208	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Dactylopiibacterium	95.0	99.96	99.89	0.99	0.97	4	-
GCA_002422685.1	s__Thauera sp002422685	77.9814	299	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	77.9604	360	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911595.1	s__Azoarcus_D sp013911595	77.7407	184	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718265.1	s__Uliginosibacterium sp016718265	77.7379	220	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Uliginosibacterium	95.0	98.20	98.02	0.86	0.86	3	-
GCF_003226565.1	s__Azoarcus_C communis	77.6757	230	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	99.33	98.67	0.90	0.80	3	-
GCF_018122735.1	s__Azoarcus_C sp018122735	77.5254	276	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:38,162] [INFO] GTDB search result was written to GCF_014197015.1_ASM1419701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:38,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:38,166] [INFO] DFAST_QC result json was written to GCF_014197015.1_ASM1419701v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:38,167] [INFO] DFAST_QC completed!
[2024-01-24 14:32:38,167] [INFO] Total running time: 0h1m51s