[2024-01-24 10:47:06,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,103] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd5a44a9-13ea-4c82-866a-fa97aeac9113/GCF_020034665.1_ASM2003466v1_genomic.fna.gz | prodigal -d GCF_020034665.1_ASM2003466v1_genomic.fna/cds.fna -a GCF_020034665.1_ASM2003466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:43,588] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:43,589] [INFO] Task started: HMMsearch
[2024-01-24 10:47:43,589] [INFO] Running command: hmmsearch --tblout GCF_020034665.1_ASM2003466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference/reference_markers.hmm GCF_020034665.1_ASM2003466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:43,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:43,988] [INFO] Found 6/6 markers.
[2024-01-24 10:47:44,080] [INFO] Query marker FASTA was written to GCF_020034665.1_ASM2003466v1_genomic.fna/markers.fasta
[2024-01-24 10:47:44,081] [INFO] Task started: Blastn
[2024-01-24 10:47:44,081] [INFO] Running command: blastn -query GCF_020034665.1_ASM2003466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference/reference_markers.fasta -out GCF_020034665.1_ASM2003466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:44,714] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:44,717] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:44,717] [INFO] Target genome list was writen to GCF_020034665.1_ASM2003466v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:44,727] [INFO] Task started: fastANI
[2024-01-24 10:47:44,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd5a44a9-13ea-4c82-866a-fa97aeac9113/GCF_020034665.1_ASM2003466v1_genomic.fna.gz --refList GCF_020034665.1_ASM2003466v1_genomic.fna/target_genomes.txt --output GCF_020034665.1_ASM2003466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:01,963] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:01,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:01,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:01,975] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:01,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:01,975] [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 beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	100.0	2193	2194	95	conclusive
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	79.8583	1004	2194	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	79.8169	917	2194	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	79.578	838	2194	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	78.2499	530	2194	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	77.8119	456	2194	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.1688	115	2194	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	75.5778	96	2194	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.4218	56	2194	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.4115	94	2194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:01,977] [INFO] DFAST Taxonomy check result was written to GCF_020034665.1_ASM2003466v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:01,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:01,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:01,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference/checkm_data
[2024-01-24 10:48:01,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:02,041] [INFO] Task started: CheckM
[2024-01-24 10:48:02,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020034665.1_ASM2003466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020034665.1_ASM2003466v1_genomic.fna/checkm_input GCF_020034665.1_ASM2003466v1_genomic.fna/checkm_result
[2024-01-24 10:49:25,756] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:25,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:25,775] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:25,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:25,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020034665.1_ASM2003466v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:25,776] [INFO] Task started: Blastn
[2024-01-24 10:49:25,776] [INFO] Running command: blastn -query GCF_020034665.1_ASM2003466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c5b34c-a5e1-4429-aab2-e9b1fb54ff01/dqc_reference/reference_markers_gtdb.fasta -out GCF_020034665.1_ASM2003466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:26,574] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:26,577] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:26,577] [INFO] Target genome list was writen to GCF_020034665.1_ASM2003466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:26,587] [INFO] Task started: fastANI
[2024-01-24 10:49:26,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd5a44a9-13ea-4c82-866a-fa97aeac9113/GCF_020034665.1_ASM2003466v1_genomic.fna.gz --refList GCF_020034665.1_ASM2003466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020034665.1_ASM2003466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:40,450] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:40,461] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:40,461] [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_000374125.1	s__Niabella aurantiaca	79.8055	919	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744715.1	s__Niabella sp017744715	79.7351	976	2194	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	79.5827	838	2194	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	78.2431	531	2194	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	77.8119	456	2194	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	77.3992	394	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720745.1	s__JJ008 sp016720745	76.5343	93	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.76	98.76	0.93	0.93	2	-
GCA_017303855.1	s__JJ008 sp017303855	76.2682	97	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331705.1	s__JJ008 sp011331705	76.215	50	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192105.1	s__JJ008 sp016192105	76.1312	113	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243445.1	s__46-32 sp003243445	76.051	112	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898405.1	s__46-32 sp001898405	75.9856	128	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
GCA_014879565.1	s__JJ008 sp014879565	75.8729	113	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	75.5858	95	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:40,463] [INFO] GTDB search result was written to GCF_020034665.1_ASM2003466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:40,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:40,466] [INFO] DFAST_QC result json was written to GCF_020034665.1_ASM2003466v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:40,466] [INFO] DFAST_QC completed!
[2024-01-24 10:49:40,467] [INFO] Total running time: 0h2m34s