[2024-01-25 17:38:35,595] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:35,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:35,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference
[2024-01-25 17:38:36,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:36,741] [INFO] Task started: Prodigal
[2024-01-25 17:38:36,741] [INFO] Running command: gunzip -c /var/lib/cwl/stgdeaa0121-7b1e-4e20-87da-2d830982b4c1/GCF_021538615.1_ASM2153861v1_genomic.fna.gz | prodigal -d GCF_021538615.1_ASM2153861v1_genomic.fna/cds.fna -a GCF_021538615.1_ASM2153861v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:02,651] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:02,651] [INFO] Task started: HMMsearch
[2024-01-25 17:39:02,651] [INFO] Running command: hmmsearch --tblout GCF_021538615.1_ASM2153861v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference/reference_markers.hmm GCF_021538615.1_ASM2153861v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:02,930] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:02,932] [INFO] Found 6/6 markers.
[2024-01-25 17:39:02,978] [INFO] Query marker FASTA was written to GCF_021538615.1_ASM2153861v1_genomic.fna/markers.fasta
[2024-01-25 17:39:02,978] [INFO] Task started: Blastn
[2024-01-25 17:39:02,978] [INFO] Running command: blastn -query GCF_021538615.1_ASM2153861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference/reference_markers.fasta -out GCF_021538615.1_ASM2153861v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:03,527] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:03,533] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:03,534] [INFO] Target genome list was writen to GCF_021538615.1_ASM2153861v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:03,537] [INFO] Task started: fastANI
[2024-01-25 17:39:03,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeaa0121-7b1e-4e20-87da-2d830982b4c1/GCF_021538615.1_ASM2153861v1_genomic.fna.gz --refList GCF_021538615.1_ASM2153861v1_genomic.fna/target_genomes.txt --output GCF_021538615.1_ASM2153861v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:14,617] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:14,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:14,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:14,626] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:14,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:14,626] [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
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	84.0923	1491	2085	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	80.3182	1017	2085	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	79.8606	967	2085	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	79.4959	930	2085	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	77.9448	455	2085	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	77.8486	489	2085	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	76.7216	100	2085	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.2069	65	2085	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.3278	89	2085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:14,628] [INFO] DFAST Taxonomy check result was written to GCF_021538615.1_ASM2153861v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:14,628] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:14,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:14,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference/checkm_data
[2024-01-25 17:39:14,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:14,688] [INFO] Task started: CheckM
[2024-01-25 17:39:14,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021538615.1_ASM2153861v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021538615.1_ASM2153861v1_genomic.fna/checkm_input GCF_021538615.1_ASM2153861v1_genomic.fna/checkm_result
[2024-01-25 17:40:23,956] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:23,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:23,977] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:23,977] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:23,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021538615.1_ASM2153861v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:23,979] [INFO] Task started: Blastn
[2024-01-25 17:40:23,979] [INFO] Running command: blastn -query GCF_021538615.1_ASM2153861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ef13ea-3a87-4beb-b826-aaa5b68dfdbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021538615.1_ASM2153861v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:24,820] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:24,823] [INFO] Selected 13 target genomes.
[2024-01-25 17:40:24,823] [INFO] Target genome list was writen to GCF_021538615.1_ASM2153861v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:24,840] [INFO] Task started: fastANI
[2024-01-25 17:40:24,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeaa0121-7b1e-4e20-87da-2d830982b4c1/GCF_021538615.1_ASM2153861v1_genomic.fna.gz --refList GCF_021538615.1_ASM2153861v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021538615.1_ASM2153861v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:37,797] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:37,806] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:40:37,806] [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_017744715.1	s__Niabella sp017744715	84.6226	1509	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101395.1	s__Niabella drilacis	80.3125	1018	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374125.1	s__Niabella aurantiaca	79.8725	964	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654455.1	s__Niabella ginsenosidivorans	77.896	491	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243115.2	s__Niabella soli	77.8887	457	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744795.1	s__Niabella sp017744795	77.477	382	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879565.1	s__JJ008 sp014879565	76.2061	82	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898405.1	s__46-32 sp001898405	76.175	104	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
GCF_012641275.1	s__Chitinophaga varians_A	76.1741	57	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595685.1	s__Flavihumibacter sp018595685	76.1408	64	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868455.1	s__JJ008 sp016868455	76.0119	68	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297075.1	s__Sediminibacterium sp004297075	75.6601	54	2085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.05	98.05	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:37,807] [INFO] GTDB search result was written to GCF_021538615.1_ASM2153861v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:37,808] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:37,815] [INFO] DFAST_QC result json was written to GCF_021538615.1_ASM2153861v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:37,815] [INFO] DFAST_QC completed!
[2024-01-25 17:40:37,815] [INFO] Total running time: 0h2m2s