[2023-06-28 12:02:01,495] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:01,498] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:01,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference
[2023-06-28 12:02:02,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:02,886] [INFO] Task started: Prodigal
[2023-06-28 12:02:02,886] [INFO] Running command: gunzip -c /var/lib/cwl/stga77c9b9f-5a68-43c7-a5bb-395a7b381144/GCA_005880435.1_ASM588043v1_genomic.fna.gz | prodigal -d GCA_005880435.1_ASM588043v1_genomic.fna/cds.fna -a GCA_005880435.1_ASM588043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:19,183] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:19,183] [INFO] Task started: HMMsearch
[2023-06-28 12:02:19,183] [INFO] Running command: hmmsearch --tblout GCA_005880435.1_ASM588043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference/reference_markers.hmm GCA_005880435.1_ASM588043v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:19,444] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:19,446] [INFO] Found 6/6 markers.
[2023-06-28 12:02:19,481] [INFO] Query marker FASTA was written to GCA_005880435.1_ASM588043v1_genomic.fna/markers.fasta
[2023-06-28 12:02:19,481] [INFO] Task started: Blastn
[2023-06-28 12:02:19,482] [INFO] Running command: blastn -query GCA_005880435.1_ASM588043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference/reference_markers.fasta -out GCA_005880435.1_ASM588043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:20,159] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:20,164] [INFO] Selected 20 target genomes.
[2023-06-28 12:02:20,165] [INFO] Target genome list was writen to GCA_005880435.1_ASM588043v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:20,173] [INFO] Task started: fastANI
[2023-06-28 12:02:20,173] [INFO] Running command: fastANI --query /var/lib/cwl/stga77c9b9f-5a68-43c7-a5bb-395a7b381144/GCA_005880435.1_ASM588043v1_genomic.fna.gz --refList GCA_005880435.1_ASM588043v1_genomic.fna/target_genomes.txt --output GCA_005880435.1_ASM588043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:31,941] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:31,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:31,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:31,953] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:31,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:02:31,953] [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
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	75.143	53	938	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	74.9387	77	938	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	74.9182	54	938	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.8839	97	938	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	74.8683	62	938	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.8498	96	938	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	74.7444	93	938	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:02:31,956] [INFO] DFAST Taxonomy check result was written to GCA_005880435.1_ASM588043v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:31,956] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:31,956] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:31,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference/checkm_data
[2023-06-28 12:02:31,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:31,997] [INFO] Task started: CheckM
[2023-06-28 12:02:31,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005880435.1_ASM588043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005880435.1_ASM588043v1_genomic.fna/checkm_input GCA_005880435.1_ASM588043v1_genomic.fna/checkm_result
[2023-06-28 12:03:18,200] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:18,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:18,226] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:18,226] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:18,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005880435.1_ASM588043v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:18,228] [INFO] Task started: Blastn
[2023-06-28 12:03:18,228] [INFO] Running command: blastn -query GCA_005880435.1_ASM588043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bbc067e-66f7-4950-9efe-c12c795e54ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_005880435.1_ASM588043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:19,154] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:19,158] [INFO] Selected 20 target genomes.
[2023-06-28 12:03:19,158] [INFO] Target genome list was writen to GCA_005880435.1_ASM588043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:19,176] [INFO] Task started: fastANI
[2023-06-28 12:03:19,177] [INFO] Running command: fastANI --query /var/lib/cwl/stga77c9b9f-5a68-43c7-a5bb-395a7b381144/GCA_005880435.1_ASM588043v1_genomic.fna.gz --refList GCA_005880435.1_ASM588043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005880435.1_ASM588043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:30,824] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:30,837] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:03:30,837] [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_005880695.1	s__VBGR01 sp005880695	99.4545	826	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__VBGR01	95.0	99.40	99.35	0.94	0.93	3	conclusive
GCA_005881155.1	s__CF-105 sp005881155	78.7052	355	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__CF-105	95.0	98.89	98.89	0.81	0.81	2	-
GCA_002427995.1	s__UBA6019 sp002427995	77.7056	214	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__UBA6019	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404015.1	s__UBA4736 sp002404015	77.2707	223	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__UBA4736	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879985.1	s__CF-118 sp005879985	77.0801	161	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__CF-118	95.0	99.16	99.16	0.85	0.85	2	-
GCA_005880795.1	s__40CM-4-65-16 sp005880795	77.062	175	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	99.34	99.06	0.87	0.86	4	-
GCA_005880855.1	s__UBA10449 sp005880855	77.0558	151	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__UBA10449	95.0	99.07	99.07	0.87	0.87	2	-
GCA_005879675.1	s__40CM-4-65-16 sp005879675	76.9993	150	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299235.1	s__Palsa-870 sp004299235	76.9828	183	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__Palsa-870	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880525.1	s__CF-118 sp005880525	76.803	134	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__CF-118	95.0	97.95	97.81	0.79	0.75	3	-
GCA_005880175.1	s__CF-161 sp005880175	76.8028	248	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__CF-161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169845.1	s__Palsa-870 sp003169845	76.7847	159	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__Palsa-870	95.0	99.95	99.95	0.97	0.97	2	-
GCA_003446775.1	s__UBA10449 sp003446775	76.7419	152	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__UBA10449	95.0	99.60	99.60	0.89	0.89	2	-
GCA_005880345.1	s__40CM-4-65-16 sp005880345	76.6421	110	938	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__Dormibacterales;f__Dormibacteraceae;g__40CM-4-65-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	75.162	67	938	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:30,839] [INFO] GTDB search result was written to GCA_005880435.1_ASM588043v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:30,840] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:30,843] [INFO] DFAST_QC result json was written to GCA_005880435.1_ASM588043v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:30,844] [INFO] DFAST_QC completed!
[2023-06-28 12:03:30,844] [INFO] Total running time: 0h1m29s