[2023-06-28 04:37:30,864] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:37:30,866] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:37:30,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference
[2023-06-28 04:37:32,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:32,062] [INFO] Task started: Prodigal
[2023-06-28 04:37:32,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg94b6dbd5-1f4b-479e-9f30-d69ed35b6776/GCA_017856655.1_ASM1785665v1_genomic.fna.gz | prodigal -d GCA_017856655.1_ASM1785665v1_genomic.fna/cds.fna -a GCA_017856655.1_ASM1785665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:43,739] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:43,739] [INFO] Task started: HMMsearch
[2023-06-28 04:37:43,739] [INFO] Running command: hmmsearch --tblout GCA_017856655.1_ASM1785665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference/reference_markers.hmm GCA_017856655.1_ASM1785665v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:43,947] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:43,948] [INFO] Found 6/6 markers.
[2023-06-28 04:37:43,974] [INFO] Query marker FASTA was written to GCA_017856655.1_ASM1785665v1_genomic.fna/markers.fasta
[2023-06-28 04:37:43,974] [INFO] Task started: Blastn
[2023-06-28 04:37:43,974] [INFO] Running command: blastn -query GCA_017856655.1_ASM1785665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference/reference_markers.fasta -out GCA_017856655.1_ASM1785665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:44,614] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:44,618] [INFO] Selected 24 target genomes.
[2023-06-28 04:37:44,619] [INFO] Target genome list was writen to GCA_017856655.1_ASM1785665v1_genomic.fna/target_genomes.txt
[2023-06-28 04:37:44,621] [INFO] Task started: fastANI
[2023-06-28 04:37:44,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg94b6dbd5-1f4b-479e-9f30-d69ed35b6776/GCA_017856655.1_ASM1785665v1_genomic.fna.gz --refList GCA_017856655.1_ASM1785665v1_genomic.fna/target_genomes.txt --output GCA_017856655.1_ASM1785665v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:38:00,420] [INFO] Task succeeded: fastANI
[2023-06-28 04:38:00,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:38:00,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:38:00,430] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:38:00,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:38:00,431] [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
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.8569	53	665	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.5435	50	665	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.1519	62	665	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.9723	53	665	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	75.7702	60	665	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	75.2535	52	665	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2223	95	665	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.0173	62	665	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	74.9006	65	665	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	74.6838	76	665	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:38:00,433] [INFO] DFAST Taxonomy check result was written to GCA_017856655.1_ASM1785665v1_genomic.fna/tc_result.tsv
[2023-06-28 04:38:00,433] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:38:00,433] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:38:00,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference/checkm_data
[2023-06-28 04:38:00,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:38:00,463] [INFO] Task started: CheckM
[2023-06-28 04:38:00,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017856655.1_ASM1785665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017856655.1_ASM1785665v1_genomic.fna/checkm_input GCA_017856655.1_ASM1785665v1_genomic.fna/checkm_result
[2023-06-28 04:38:36,534] [INFO] Task succeeded: CheckM
[2023-06-28 04:38:36,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 04:38:36,556] [INFO] ===== Completeness check finished =====
[2023-06-28 04:38:36,556] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:38:36,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017856655.1_ASM1785665v1_genomic.fna/markers.fasta)
[2023-06-28 04:38:36,557] [INFO] Task started: Blastn
[2023-06-28 04:38:36,557] [INFO] Running command: blastn -query GCA_017856655.1_ASM1785665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb9da23-86cb-4167-ab0c-3b9a39bf3196/dqc_reference/reference_markers_gtdb.fasta -out GCA_017856655.1_ASM1785665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:38:37,526] [INFO] Task succeeded: Blastn
[2023-06-28 04:38:37,529] [INFO] Selected 9 target genomes.
[2023-06-28 04:38:37,529] [INFO] Target genome list was writen to GCA_017856655.1_ASM1785665v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:38:37,534] [INFO] Task started: fastANI
[2023-06-28 04:38:37,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg94b6dbd5-1f4b-479e-9f30-d69ed35b6776/GCA_017856655.1_ASM1785665v1_genomic.fna.gz --refList GCA_017856655.1_ASM1785665v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017856655.1_ASM1785665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:38:41,487] [INFO] Task succeeded: fastANI
[2023-06-28 04:38:41,501] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:38:41,501] [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_903860195.1	s__UBA953 sp903860195	98.556	513	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.96	98.57	0.86	0.84	5	conclusive
GCA_016871415.1	s__UBA953 sp016871415	84.5016	543	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871725.1	s__UBA953 sp016871725	81.8937	431	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293385.1	s__UBA953 sp004293385	81.6314	196	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569245.1	s__UBA953 sp003569245	81.2247	410	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798925.1	s__UBA953 sp005798925	81.0166	320	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913915.1	s__UBA953 sp903913915	80.6592	395	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.51	99.16	0.93	0.89	3	-
GCA_014193315.1	s__UBA953 sp003569405	79.8706	330	665	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.72	96.62	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-28 04:38:41,503] [INFO] GTDB search result was written to GCA_017856655.1_ASM1785665v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:38:41,503] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:38:41,506] [INFO] DFAST_QC result json was written to GCA_017856655.1_ASM1785665v1_genomic.fna/dqc_result.json
[2023-06-28 04:38:41,507] [INFO] DFAST_QC completed!
[2023-06-28 04:38:41,507] [INFO] Total running time: 0h1m11s