[2023-06-19 10:30:02,130] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:30:02,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:30:02,132] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference
[2023-06-19 10:30:03,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:30:03,550] [INFO] Task started: Prodigal
[2023-06-19 10:30:03,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dd8e030-0a7b-462f-9ed5-72be9ad560e4/GCA_018267065.1_ASM1826706v1_genomic.fna.gz | prodigal -d GCA_018267065.1_ASM1826706v1_genomic.fna/cds.fna -a GCA_018267065.1_ASM1826706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:30:30,694] [INFO] Task succeeded: Prodigal
[2023-06-19 10:30:30,695] [INFO] Task started: HMMsearch
[2023-06-19 10:30:30,695] [INFO] Running command: hmmsearch --tblout GCA_018267065.1_ASM1826706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference/reference_markers.hmm GCA_018267065.1_ASM1826706v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:30:30,956] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:30:30,958] [INFO] Found 6/6 markers.
[2023-06-19 10:30:30,988] [INFO] Query marker FASTA was written to GCA_018267065.1_ASM1826706v1_genomic.fna/markers.fasta
[2023-06-19 10:30:30,989] [INFO] Task started: Blastn
[2023-06-19 10:30:30,989] [INFO] Running command: blastn -query GCA_018267065.1_ASM1826706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference/reference_markers.fasta -out GCA_018267065.1_ASM1826706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:30:31,625] [INFO] Task succeeded: Blastn
[2023-06-19 10:30:31,630] [INFO] Selected 27 target genomes.
[2023-06-19 10:30:31,630] [INFO] Target genome list was writen to GCA_018267065.1_ASM1826706v1_genomic.fna/target_genomes.txt
[2023-06-19 10:30:31,634] [INFO] Task started: fastANI
[2023-06-19 10:30:31,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd8e030-0a7b-462f-9ed5-72be9ad560e4/GCA_018267065.1_ASM1826706v1_genomic.fna.gz --refList GCA_018267065.1_ASM1826706v1_genomic.fna/target_genomes.txt --output GCA_018267065.1_ASM1826706v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:30:50,523] [INFO] Task succeeded: fastANI
[2023-06-19 10:30:50,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:30:50,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:30:50,532] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:30:50,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:30:50,533] [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
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	76.1547	69	943	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	75.9295	60	943	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:30:50,535] [INFO] DFAST Taxonomy check result was written to GCA_018267065.1_ASM1826706v1_genomic.fna/tc_result.tsv
[2023-06-19 10:30:50,536] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:30:50,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:30:50,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference/checkm_data
[2023-06-19 10:30:50,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:30:50,581] [INFO] Task started: CheckM
[2023-06-19 10:30:50,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267065.1_ASM1826706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267065.1_ASM1826706v1_genomic.fna/checkm_input GCA_018267065.1_ASM1826706v1_genomic.fna/checkm_result
[2023-06-19 10:32:03,798] [INFO] Task succeeded: CheckM
[2023-06-19 10:32:03,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:32:03,824] [INFO] ===== Completeness check finished =====
[2023-06-19 10:32:03,825] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:32:03,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267065.1_ASM1826706v1_genomic.fna/markers.fasta)
[2023-06-19 10:32:03,825] [INFO] Task started: Blastn
[2023-06-19 10:32:03,826] [INFO] Running command: blastn -query GCA_018267065.1_ASM1826706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0b59e31-eb05-4284-b46f-326299eb26ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267065.1_ASM1826706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:32:04,758] [INFO] Task succeeded: Blastn
[2023-06-19 10:32:04,763] [INFO] Selected 9 target genomes.
[2023-06-19 10:32:04,764] [INFO] Target genome list was writen to GCA_018267065.1_ASM1826706v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:32:04,768] [INFO] Task started: fastANI
[2023-06-19 10:32:04,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd8e030-0a7b-462f-9ed5-72be9ad560e4/GCA_018267065.1_ASM1826706v1_genomic.fna.gz --refList GCA_018267065.1_ASM1826706v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267065.1_ASM1826706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:32:11,179] [INFO] Task succeeded: fastANI
[2023-06-19 10:32:11,195] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:32:11,196] [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_018267065.1	s__PHOS-HE28 sp018267065	99.9999	927	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018266685.1	s__PHOS-HE28 sp018266685	87.864	748	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.70	99.70	0.93	0.93	2	-
GCA_018266475.1	s__PHOS-HE28 sp018266475	81.4654	541	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057455.1	s__PHOS-HE28 sp018057455	81.0563	528	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.80	99.80	0.93	0.93	2	-
GCA_016700415.1	s__PHOS-HE28 sp002396605	80.0826	480	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.63	99.43	0.98	0.96	12	-
GCA_018267055.1	s__PHOS-HE28 sp018267055	79.7545	420	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719225.1	s__PHOS-HE28 sp016719225	78.8374	343	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788485.1	s__PHOS-HE28 sp016788485	78.7138	290	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788405.1	s__PHOS-HE28 sp016788405	77.9936	163	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:32:11,198] [INFO] GTDB search result was written to GCA_018267065.1_ASM1826706v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:32:11,199] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:32:11,203] [INFO] DFAST_QC result json was written to GCA_018267065.1_ASM1826706v1_genomic.fna/dqc_result.json
[2023-06-19 10:32:11,204] [INFO] DFAST_QC completed!
[2023-06-19 10:32:11,204] [INFO] Total running time: 0h2m9s