[2023-06-18 18:10:27,768] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:27,782] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:27,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference
[2023-06-18 18:10:31,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:31,859] [INFO] Task started: Prodigal
[2023-06-18 18:10:31,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg42867bbd-4604-4e9e-9275-ea63e94abd0f/GCA_018369055.1_ASM1836905v1_genomic.fna.gz | prodigal -d GCA_018369055.1_ASM1836905v1_genomic.fna/cds.fna -a GCA_018369055.1_ASM1836905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:42,565] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:42,565] [INFO] Task started: HMMsearch
[2023-06-18 18:10:42,566] [INFO] Running command: hmmsearch --tblout GCA_018369055.1_ASM1836905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference/reference_markers.hmm GCA_018369055.1_ASM1836905v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:42,798] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:42,799] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg42867bbd-4604-4e9e-9275-ea63e94abd0f/GCA_018369055.1_ASM1836905v1_genomic.fna.gz]
[2023-06-18 18:10:42,854] [INFO] Query marker FASTA was written to GCA_018369055.1_ASM1836905v1_genomic.fna/markers.fasta
[2023-06-18 18:10:42,854] [INFO] Task started: Blastn
[2023-06-18 18:10:42,855] [INFO] Running command: blastn -query GCA_018369055.1_ASM1836905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference/reference_markers.fasta -out GCA_018369055.1_ASM1836905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:44,334] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:44,356] [INFO] Selected 26 target genomes.
[2023-06-18 18:10:44,356] [INFO] Target genome list was writen to GCA_018369055.1_ASM1836905v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:44,360] [INFO] Task started: fastANI
[2023-06-18 18:10:44,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg42867bbd-4604-4e9e-9275-ea63e94abd0f/GCA_018369055.1_ASM1836905v1_genomic.fna.gz --refList GCA_018369055.1_ASM1836905v1_genomic.fna/target_genomes.txt --output GCA_018369055.1_ASM1836905v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:11:01,399] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:01,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:11:01,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:11:01,405] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 18:11:01,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 18:11:01,406] [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
Victivallis lenta	strain=BBE-744-WT-12	GCA_009695545.1	2606640	2606640	type	True	98.4223	1261	1436	95	conclusive
Victivallis vadensis	strain=DSM 14823	GCA_003096415.1	172901	172901	type	True	80.2623	502	1436	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	74.6971	50	1436	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	74.5968	64	1436	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:11:01,409] [INFO] DFAST Taxonomy check result was written to GCA_018369055.1_ASM1836905v1_genomic.fna/tc_result.tsv
[2023-06-18 18:11:01,410] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:11:01,411] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:11:01,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference/checkm_data
[2023-06-18 18:11:01,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:11:01,457] [INFO] Task started: CheckM
[2023-06-18 18:11:01,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018369055.1_ASM1836905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018369055.1_ASM1836905v1_genomic.fna/checkm_input GCA_018369055.1_ASM1836905v1_genomic.fna/checkm_result
[2023-06-18 18:11:35,937] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:35,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:35,966] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:35,966] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:35,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018369055.1_ASM1836905v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:35,967] [INFO] Task started: Blastn
[2023-06-18 18:11:35,967] [INFO] Running command: blastn -query GCA_018369055.1_ASM1836905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b9c6dab-d4b6-4c4a-8c05-0e7074fae9eb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018369055.1_ASM1836905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:37,017] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:37,021] [INFO] Selected 12 target genomes.
[2023-06-18 18:11:37,021] [INFO] Target genome list was writen to GCA_018369055.1_ASM1836905v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:37,070] [INFO] Task started: fastANI
[2023-06-18 18:11:37,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg42867bbd-4604-4e9e-9275-ea63e94abd0f/GCA_018369055.1_ASM1836905v1_genomic.fna.gz --refList GCA_018369055.1_ASM1836905v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018369055.1_ASM1836905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:45,010] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:45,019] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:11:45,019] [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_009695545.1	s__Victivallis lenta	98.4223	1261	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.99	98.42	0.92	0.87	10	conclusive
GCA_018265615.1	s__Victivallis sp018265615	81.8862	729	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096415.1	s__Victivallis vadensis	80.2965	500	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.78	98.45	0.89	0.85	7	-
GCA_900551245.1	s__Victivallis sp900551245	78.9804	369	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	98.16	98.16	0.84	0.84	2	-
GCA_900550905.1	s__Victivallis sp900550905	78.5186	315	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900768515.1	s__Victivallis sp900768515	78.4838	310	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__Victivallis	95.0	99.40	99.40	0.89	0.89	2	-
GCA_002314455.1	s__UBA1784 sp002314455	76.9803	79	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__UBA1784	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292515.1	s__UBA1784 sp016292515	76.8702	68	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__UBA1784	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017450705.1	s__UBA1784 sp017450705	76.3775	116	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__UBA1784	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443585.1	s__UBA1784 sp017443585	76.1173	96	1436	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__Victivallaceae;g__UBA1784	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:11:45,021] [INFO] GTDB search result was written to GCA_018369055.1_ASM1836905v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:45,022] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:45,025] [INFO] DFAST_QC result json was written to GCA_018369055.1_ASM1836905v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:45,025] [INFO] DFAST_QC completed!
[2023-06-18 18:11:45,025] [INFO] Total running time: 0h1m17s