[2024-01-24 15:27:12,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference
[2024-01-24 15:27:14,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:14,069] [INFO] Task started: Prodigal
[2024-01-24 15:27:14,070] [INFO] Running command: gunzip -c /var/lib/cwl/stgc23e0dc3-b360-43a2-beff-fe93a6e1caaa/GCF_013266755.1_ASM1326675v1_genomic.fna.gz | prodigal -d GCF_013266755.1_ASM1326675v1_genomic.fna/cds.fna -a GCF_013266755.1_ASM1326675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:39,543] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:39,544] [INFO] Task started: HMMsearch
[2024-01-24 15:27:39,544] [INFO] Running command: hmmsearch --tblout GCF_013266755.1_ASM1326675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference/reference_markers.hmm GCF_013266755.1_ASM1326675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:39,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:39,997] [INFO] Found 6/6 markers.
[2024-01-24 15:27:40,065] [INFO] Query marker FASTA was written to GCF_013266755.1_ASM1326675v1_genomic.fna/markers.fasta
[2024-01-24 15:27:40,066] [INFO] Task started: Blastn
[2024-01-24 15:27:40,066] [INFO] Running command: blastn -query GCF_013266755.1_ASM1326675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference/reference_markers.fasta -out GCF_013266755.1_ASM1326675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:41,160] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:41,164] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:41,164] [INFO] Target genome list was writen to GCF_013266755.1_ASM1326675v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:41,174] [INFO] Task started: fastANI
[2024-01-24 15:27:41,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgc23e0dc3-b360-43a2-beff-fe93a6e1caaa/GCF_013266755.1_ASM1326675v1_genomic.fna.gz --refList GCF_013266755.1_ASM1326675v1_genomic.fna/target_genomes.txt --output GCF_013266755.1_ASM1326675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:05,903] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:05,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:05,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:05,919] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:28:05,919] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:28:05,919] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.2022	863	2652	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	81.2	894	2652	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.6521	955	2652	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.5923	966	2652	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.5256	806	2652	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.4982	822	2652	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.4737	830	2652	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.1369	853	2652	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	80.0542	837	2652	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.964	873	2652	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.7352	824	2652	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.7256	921	2652	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.4759	713	2652	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.4085	703	2652	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.238	1044	2652	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.1747	823	2652	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.1561	992	2652	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.1352	1018	2652	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.6988	903	2652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:05,923] [INFO] DFAST Taxonomy check result was written to GCF_013266755.1_ASM1326675v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:05,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:05,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:05,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference/checkm_data
[2024-01-24 15:28:05,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:06,000] [INFO] Task started: CheckM
[2024-01-24 15:28:06,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013266755.1_ASM1326675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013266755.1_ASM1326675v1_genomic.fna/checkm_input GCF_013266755.1_ASM1326675v1_genomic.fna/checkm_result
[2024-01-24 15:30:39,652] [INFO] Task succeeded: CheckM
[2024-01-24 15:30:39,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:30:39,684] [INFO] ===== Completeness check finished =====
[2024-01-24 15:30:39,684] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:30:39,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013266755.1_ASM1326675v1_genomic.fna/markers.fasta)
[2024-01-24 15:30:39,685] [INFO] Task started: Blastn
[2024-01-24 15:30:39,685] [INFO] Running command: blastn -query GCF_013266755.1_ASM1326675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72f13527-d562-48bc-9be9-3f4a8107c134/dqc_reference/reference_markers_gtdb.fasta -out GCF_013266755.1_ASM1326675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:30:41,906] [INFO] Task succeeded: Blastn
[2024-01-24 15:30:41,910] [INFO] Selected 19 target genomes.
[2024-01-24 15:30:41,910] [INFO] Target genome list was writen to GCF_013266755.1_ASM1326675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:30:41,925] [INFO] Task started: fastANI
[2024-01-24 15:30:41,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgc23e0dc3-b360-43a2-beff-fe93a6e1caaa/GCF_013266755.1_ASM1326675v1_genomic.fna.gz --refList GCF_013266755.1_ASM1326675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013266755.1_ASM1326675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:31:12,248] [INFO] Task succeeded: fastANI
[2024-01-24 15:31:12,269] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:31:12,270] [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_013266755.1	s__Aquabacterium_A terrae	100.0	2647	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016213205.1	s__Aquabacterium_A sp016213205	81.9757	1175	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	81.6062	943	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	81.1984	1155	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770815.1	s__Aquabacterium_A sp001770815	81.1748	951	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	81.1621	868	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.9984	1123	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	80.9643	856	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCF_005403045.1	s__Aquabacterium_A pictum	80.8242	1111	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075165.1	s__JAEUPI01 sp015075165	80.6883	976	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAEUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	80.6864	815	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	80.5569	788	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583785.1	s__Rubrivivax gelatinosus_B	80.4461	929	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.02	99.02	0.92	0.92	2	-
GCA_017999135.1	s__Aquabacterium_A sp017999135	80.3928	601	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971105.1	s__Rubrivivax sp018971105	80.3457	761	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.2535	1013	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425905.1	s__Methylibium sp001425905	80.1888	809	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191995.1	s__Rubrivivax sp016191995	80.0997	816	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789955.1	s__Rubrivivax sp016789955	79.7184	940	2652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:31:12,272] [INFO] GTDB search result was written to GCF_013266755.1_ASM1326675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:31:12,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:31:12,284] [INFO] DFAST_QC result json was written to GCF_013266755.1_ASM1326675v1_genomic.fna/dqc_result.json
[2024-01-24 15:31:12,284] [INFO] DFAST_QC completed!
[2024-01-24 15:31:12,284] [INFO] Total running time: 0h3m60s