[2024-01-24 13:45:45,648] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,650] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference
[2024-01-24 13:45:47,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,189] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,189] [INFO] Running command: gunzip -c /var/lib/cwl/stg758f7d39-f877-4d17-9be1-4cb86618d044/GCF_008107625.1_ASM810762v1_genomic.fna.gz | prodigal -d GCF_008107625.1_ASM810762v1_genomic.fna/cds.fna -a GCF_008107625.1_ASM810762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:04,892] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:04,893] [INFO] Task started: HMMsearch
[2024-01-24 13:46:04,893] [INFO] Running command: hmmsearch --tblout GCF_008107625.1_ASM810762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference/reference_markers.hmm GCF_008107625.1_ASM810762v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:05,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:05,245] [INFO] Found 6/6 markers.
[2024-01-24 13:46:05,304] [INFO] Query marker FASTA was written to GCF_008107625.1_ASM810762v1_genomic.fna/markers.fasta
[2024-01-24 13:46:05,304] [INFO] Task started: Blastn
[2024-01-24 13:46:05,305] [INFO] Running command: blastn -query GCF_008107625.1_ASM810762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference/reference_markers.fasta -out GCF_008107625.1_ASM810762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:06,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:06,277] [INFO] Selected 25 target genomes.
[2024-01-24 13:46:06,277] [INFO] Target genome list was writen to GCF_008107625.1_ASM810762v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:06,290] [INFO] Task started: fastANI
[2024-01-24 13:46:06,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg758f7d39-f877-4d17-9be1-4cb86618d044/GCF_008107625.1_ASM810762v1_genomic.fna.gz --refList GCF_008107625.1_ASM810762v1_genomic.fna/target_genomes.txt --output GCF_008107625.1_ASM810762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:26,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:26,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:26,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:27,029] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:27,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:27,031] [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
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	99.997	1822	1836	95	conclusive
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	83.6761	1089	1836	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	83.2838	859	1836	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.8017	501	1836	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.4349	451	1836	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.4343	477	1836	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.3339	464	1836	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.1885	443	1836	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.1838	460	1836	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	79.1582	445	1836	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	79.1413	451	1836	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	79.1045	500	1836	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	79.0837	395	1836	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.9054	457	1836	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.8461	483	1836	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.2318	347	1836	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.3657	247	1836	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1359	251	1836	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.1127	113	1836	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	75.9391	122	1836	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	75.5391	51	1836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:27,034] [INFO] DFAST Taxonomy check result was written to GCF_008107625.1_ASM810762v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:27,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:27,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:27,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference/checkm_data
[2024-01-24 13:46:27,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:27,214] [INFO] Task started: CheckM
[2024-01-24 13:46:27,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008107625.1_ASM810762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008107625.1_ASM810762v1_genomic.fna/checkm_input GCF_008107625.1_ASM810762v1_genomic.fna/checkm_result
[2024-01-24 13:47:23,126] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:23,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,151] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:23,151] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:23,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008107625.1_ASM810762v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:23,152] [INFO] Task started: Blastn
[2024-01-24 13:47:23,152] [INFO] Running command: blastn -query GCF_008107625.1_ASM810762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ef45d6c-7ca5-4654-9c2d-7a0f1bfab31a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008107625.1_ASM810762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:24,833] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:24,838] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:24,839] [INFO] Target genome list was writen to GCF_008107625.1_ASM810762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:24,858] [INFO] Task started: fastANI
[2024-01-24 13:47:24,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg758f7d39-f877-4d17-9be1-4cb86618d044/GCF_008107625.1_ASM810762v1_genomic.fna.gz --refList GCF_008107625.1_ASM810762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008107625.1_ASM810762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:44,653] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:44,680] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:44,680] [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_008107625.1	s__Zoogloea oleivorans	99.997	1823	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016720685.1	s__Zoogloea sp016720685	84.0059	877	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	83.6969	1086	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026175.1	s__Zoogloea sp009026175	83.4867	890	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	83.3522	957	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539865.1	s__Zoogloea ramigera	83.3347	852	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	99.03	99.03	0.93	0.93	2	-
GCF_002028455.1	s__Zoogloea sp002028455	83.3052	1026	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241665.1	s__Zoogloea sp018241665	83.2028	1007	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241685.1	s__Zoogloea sp018241685	83.1179	979	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657735.1	s__Zoogloea sp015657735	83.0318	632	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241725.1	s__Zoogloea sp018241725	82.9305	985	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302315.1	s__Zoogloea sp017302315	82.9081	816	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789125.1	s__Zoogloea sp016789125	82.6654	655	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309145.1	s__Zoogloea sp017309145	82.6565	810	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	79.182	451	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_018524365.1	s__Denitromonas sp018524365	78.9495	522	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515535.1	s__JAAYYF01 sp012515535	74.807	65	1836	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAAYYF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,682] [INFO] GTDB search result was written to GCF_008107625.1_ASM810762v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:44,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:44,686] [INFO] DFAST_QC result json was written to GCF_008107625.1_ASM810762v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:44,687] [INFO] DFAST_QC completed!
[2024-01-24 13:47:44,687] [INFO] Total running time: 0h1m59s