[2023-06-13 23:46:01,741] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:46:01,743] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:46:01,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference
[2023-06-13 23:46:02,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:46:02,837] [INFO] Task started: Prodigal
[2023-06-13 23:46:02,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg8378cf69-2160-43b7-b0ca-de622e9fba3d/GCA_022821925.1_ASM2282192v1_genomic.fna.gz | prodigal -d GCA_022821925.1_ASM2282192v1_genomic.fna/cds.fna -a GCA_022821925.1_ASM2282192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:46:19,184] [INFO] Task succeeded: Prodigal
[2023-06-13 23:46:19,185] [INFO] Task started: HMMsearch
[2023-06-13 23:46:19,185] [INFO] Running command: hmmsearch --tblout GCA_022821925.1_ASM2282192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference/reference_markers.hmm GCA_022821925.1_ASM2282192v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:46:19,501] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:46:19,502] [INFO] Found 6/6 markers.
[2023-06-13 23:46:19,550] [INFO] Query marker FASTA was written to GCA_022821925.1_ASM2282192v1_genomic.fna/markers.fasta
[2023-06-13 23:46:19,550] [INFO] Task started: Blastn
[2023-06-13 23:46:19,550] [INFO] Running command: blastn -query GCA_022821925.1_ASM2282192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference/reference_markers.fasta -out GCA_022821925.1_ASM2282192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:46:20,155] [INFO] Task succeeded: Blastn
[2023-06-13 23:46:20,158] [INFO] Selected 24 target genomes.
[2023-06-13 23:46:20,159] [INFO] Target genome list was writen to GCA_022821925.1_ASM2282192v1_genomic.fna/target_genomes.txt
[2023-06-13 23:46:20,160] [INFO] Task started: fastANI
[2023-06-13 23:46:20,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg8378cf69-2160-43b7-b0ca-de622e9fba3d/GCA_022821925.1_ASM2282192v1_genomic.fna.gz --refList GCA_022821925.1_ASM2282192v1_genomic.fna/target_genomes.txt --output GCA_022821925.1_ASM2282192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:46:37,366] [INFO] Task succeeded: fastANI
[2023-06-13 23:46:37,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:46:37,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:46:37,374] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:46:37,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 23:46:37,375] [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 gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	74.8314	67	2046	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	74.8314	67	2046	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.8265	71	2046	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	74.8076	61	2046	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	74.7523	66	2046	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.7365	70	2046	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	74.7218	55	2046	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.6866	86	2046	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.6045	68	2046	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 23:46:37,376] [INFO] DFAST Taxonomy check result was written to GCA_022821925.1_ASM2282192v1_genomic.fna/tc_result.tsv
[2023-06-13 23:46:37,377] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:46:37,377] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:46:37,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference/checkm_data
[2023-06-13 23:46:37,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:46:37,439] [INFO] Task started: CheckM
[2023-06-13 23:46:37,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022821925.1_ASM2282192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022821925.1_ASM2282192v1_genomic.fna/checkm_input GCA_022821925.1_ASM2282192v1_genomic.fna/checkm_result
[2023-06-13 23:47:22,634] [INFO] Task succeeded: CheckM
[2023-06-13 23:47:22,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:47:22,655] [INFO] ===== Completeness check finished =====
[2023-06-13 23:47:22,656] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:47:22,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022821925.1_ASM2282192v1_genomic.fna/markers.fasta)
[2023-06-13 23:47:22,659] [INFO] Task started: Blastn
[2023-06-13 23:47:22,659] [INFO] Running command: blastn -query GCA_022821925.1_ASM2282192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16ad0d04-4705-4895-8b44-34a61fff052f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022821925.1_ASM2282192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:47:23,656] [INFO] Task succeeded: Blastn
[2023-06-13 23:47:23,659] [INFO] Selected 19 target genomes.
[2023-06-13 23:47:23,659] [INFO] Target genome list was writen to GCA_022821925.1_ASM2282192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:47:23,665] [INFO] Task started: fastANI
[2023-06-13 23:47:23,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg8378cf69-2160-43b7-b0ca-de622e9fba3d/GCA_022821925.1_ASM2282192v1_genomic.fna.gz --refList GCA_022821925.1_ASM2282192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022821925.1_ASM2282192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:47:39,995] [INFO] Task succeeded: fastANI
[2023-06-13 23:47:40,002] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:47:40,002] [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
GCA_009841225.1	s__VXMF01 sp009841225	89.0562	1382	2046	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__VXMF01	95.0	97.84	97.84	0.95	0.95	2	-
GCA_009838515.1	s__VXMF01 sp009838515	88.6848	1403	2046	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__VXMF01	95.0	99.95	99.93	0.99	0.98	3	-
GCA_016125275.1	s__RI-231 sp016125275	76.0831	209	2046	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__RI-231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716385.1	s__JADJWL01 sp016716385	75.4732	79	2046	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADJWL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825945.1	s__SYLY01 sp902825945	75.16	92	2046	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__SYLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871015.1	s__SYLY01 sp016871015	75.0451	87	2046	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__SYLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	74.9297	66	2046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025265.1	s__Conexibacter woesei	74.6836	89	2046	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	74.6082	70	2046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:47:40,004] [INFO] GTDB search result was written to GCA_022821925.1_ASM2282192v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:47:40,005] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:47:40,008] [INFO] DFAST_QC result json was written to GCA_022821925.1_ASM2282192v1_genomic.fna/dqc_result.json
[2023-06-13 23:47:40,008] [INFO] DFAST_QC completed!
[2023-06-13 23:47:40,008] [INFO] Total running time: 0h1m38s