[2024-01-24 13:37:19,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:19,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:19,781] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference
[2024-01-24 13:37:21,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:21,190] [INFO] Task started: Prodigal
[2024-01-24 13:37:21,190] [INFO] Running command: gunzip -c /var/lib/cwl/stga5eadea5-7ee8-47ff-a87e-8c4bd8653ef0/GCF_000613505.1_ASM61350v1_genomic.fna.gz | prodigal -d GCF_000613505.1_ASM61350v1_genomic.fna/cds.fna -a GCF_000613505.1_ASM61350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:37,718] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:37,718] [INFO] Task started: HMMsearch
[2024-01-24 13:37:37,718] [INFO] Running command: hmmsearch --tblout GCF_000613505.1_ASM61350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference/reference_markers.hmm GCF_000613505.1_ASM61350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:37,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:37,991] [INFO] Found 6/6 markers.
[2024-01-24 13:37:38,022] [INFO] Query marker FASTA was written to GCF_000613505.1_ASM61350v1_genomic.fna/markers.fasta
[2024-01-24 13:37:38,023] [INFO] Task started: Blastn
[2024-01-24 13:37:38,023] [INFO] Running command: blastn -query GCF_000613505.1_ASM61350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference/reference_markers.fasta -out GCF_000613505.1_ASM61350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:38,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:38,621] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:38,622] [INFO] Target genome list was writen to GCF_000613505.1_ASM61350v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:38,635] [INFO] Task started: fastANI
[2024-01-24 13:37:38,635] [INFO] Running command: fastANI --query /var/lib/cwl/stga5eadea5-7ee8-47ff-a87e-8c4bd8653ef0/GCF_000613505.1_ASM61350v1_genomic.fna.gz --refList GCF_000613505.1_ASM61350v1_genomic.fna/target_genomes.txt --output GCF_000613505.1_ASM61350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:46,025] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:46,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:46,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:46,037] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:46,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:46,038] [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
Prevotella oris	strain=JCM 12252	GCA_000613505.1	28135	28135	type	True	100.0	983	985	95	conclusive
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	99.9669	985	985	95	conclusive
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	99.9555	978	985	95	conclusive
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	81.447	432	985	95	below_threshold
Prevotella salivae	strain=DSM 15606	GCA_000185845.1	228604	228604	type	True	81.422	566	985	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	81.2212	442	985	95	below_threshold
Prevotella oulorum	strain=JCM 14966	GCA_000613785.1	28136	28136	type	True	80.5462	194	985	95	below_threshold
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	80.2791	199	985	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	80.1335	131	985	95	below_threshold
Prevotella phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	78.8377	87	985	95	below_threshold
Prevotella oralis	strain=DSM 20702	GCA_900129435.1	28134	28134	type	True	78.2269	80	985	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	77.7137	69	985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:46,040] [INFO] DFAST Taxonomy check result was written to GCF_000613505.1_ASM61350v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:46,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:46,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:46,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference/checkm_data
[2024-01-24 13:37:46,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:46,078] [INFO] Task started: CheckM
[2024-01-24 13:37:46,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613505.1_ASM61350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613505.1_ASM61350v1_genomic.fna/checkm_input GCF_000613505.1_ASM61350v1_genomic.fna/checkm_result
[2024-01-24 13:38:37,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:37,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:37,409] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:37,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:37,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613505.1_ASM61350v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:37,410] [INFO] Task started: Blastn
[2024-01-24 13:38:37,410] [INFO] Running command: blastn -query GCF_000613505.1_ASM61350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd63fd1-40ce-466c-aaec-c731dafb8b59/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613505.1_ASM61350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:38,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:38,227] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:38,228] [INFO] Target genome list was writen to GCF_000613505.1_ASM61350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:38,258] [INFO] Task started: fastANI
[2024-01-24 13:38:38,259] [INFO] Running command: fastANI --query /var/lib/cwl/stga5eadea5-7ee8-47ff-a87e-8c4bd8653ef0/GCF_000613505.1_ASM61350v1_genomic.fna.gz --refList GCF_000613505.1_ASM61350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613505.1_ASM61350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:47,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:47,562] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:47,563] [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_900637655.1	s__Prevotella oris	99.9669	985	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	conclusive
GCF_900454835.1	s__Prevotella denticola	81.97	118	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCF_000382385.1	s__Prevotella maculosa	81.4675	432	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	-
GCF_000185845.1	s__Prevotella salivae	81.4271	565	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.60	96.70	0.94	0.87	27	-
GCF_000613785.1	s__Prevotella oulorum	80.5566	193	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	-
GCF_003043925.1	s__Prevotella sp003043925	79.903	129	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001262015.1	s__Prevotella fusca	79.6365	142	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001553265.1	s__Prevotella sp001553265	79.1558	130	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.33	99.33	0.90	0.90	2	-
GCF_000177075.1	s__Prevotella buccalis	78.5089	93	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCA_018053665.1	s__Prevotella sp018053665	78.3568	107	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.38	99.32	0.87	0.85	3	-
GCF_000185145.2	s__Prevotella oralis	78.2967	78	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.13	0.96	0.92	6	-
GCF_000426585.1	s__Prevotella baroniae	77.8568	117	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
GCA_905236755.1	s__Prevotella sp905236755	77.759	96	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
GCF_000179055.1	s__Prevotella bryantii	77.5776	70	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.02	98.58	0.88	0.73	13	-
GCA_018054505.1	s__Prevotella sp018054505	77.1783	88	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	-
GCA_900547085.1	s__Prevotella sp900547085	76.5798	52	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768785.1	s__Prevotella sp902768785	76.5177	56	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.99	96.99	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,564] [INFO] GTDB search result was written to GCF_000613505.1_ASM61350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:47,565] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:47,569] [INFO] DFAST_QC result json was written to GCF_000613505.1_ASM61350v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:47,570] [INFO] DFAST_QC completed!
[2024-01-24 13:38:47,570] [INFO] Total running time: 0h1m28s