[2024-01-24 13:46:25,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,260] [INFO] DQC Reference Directory: /var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference
[2024-01-24 13:46:26,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,456] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg5058c91d-e93c-4f24-bb1c-fa01f2780d60/GCF_000185145.2_ASM18514v2_genomic.fna.gz | prodigal -d GCF_000185145.2_ASM18514v2_genomic.fna/cds.fna -a GCF_000185145.2_ASM18514v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:41,158] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:41,158] [INFO] Task started: HMMsearch
[2024-01-24 13:46:41,158] [INFO] Running command: hmmsearch --tblout GCF_000185145.2_ASM18514v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference/reference_markers.hmm GCF_000185145.2_ASM18514v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:41,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:41,410] [INFO] Found 6/6 markers.
[2024-01-24 13:46:41,435] [INFO] Query marker FASTA was written to GCF_000185145.2_ASM18514v2_genomic.fna/markers.fasta
[2024-01-24 13:46:41,436] [INFO] Task started: Blastn
[2024-01-24 13:46:41,436] [INFO] Running command: blastn -query GCF_000185145.2_ASM18514v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference/reference_markers.fasta -out GCF_000185145.2_ASM18514v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:42,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:42,084] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:42,084] [INFO] Target genome list was writen to GCF_000185145.2_ASM18514v2_genomic.fna/target_genomes.txt
[2024-01-24 13:46:42,136] [INFO] Task started: fastANI
[2024-01-24 13:46:42,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg5058c91d-e93c-4f24-bb1c-fa01f2780d60/GCF_000185145.2_ASM18514v2_genomic.fna.gz --refList GCF_000185145.2_ASM18514v2_genomic.fna/target_genomes.txt --output GCF_000185145.2_ASM18514v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:51,321] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:51,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:51,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:51,341] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:51,341] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:46:51,341] [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 oralis	strain=ATCC 33269	GCA_000185145.2	28134	28134	type	True	100.0	942	945	95	inconclusive
Prevotella oralis	strain=DSM 20702	GCA_900129435.1	28134	28134	type	True	99.976	931	945	95	inconclusive
Prevotella phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	97.1944	864	945	95	inconclusive
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	78.5648	85	945	95	below_threshold
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	78.1443	64	945	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	78.0216	81	945	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.7722	88	945	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.6005	59	945	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.8156	70	945	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.7044	63	945	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.6637	51	945	95	below_threshold
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	76.6436	59	945	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4626	52	945	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	76.4285	60	945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:51,343] [INFO] DFAST Taxonomy check result was written to GCF_000185145.2_ASM18514v2_genomic.fna/tc_result.tsv
[2024-01-24 13:46:51,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:51,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:51,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference/checkm_data
[2024-01-24 13:46:51,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:51,373] [INFO] Task started: CheckM
[2024-01-24 13:46:51,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000185145.2_ASM18514v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000185145.2_ASM18514v2_genomic.fna/checkm_input GCF_000185145.2_ASM18514v2_genomic.fna/checkm_result
[2024-01-24 13:47:36,232] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:36,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,252] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:36,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:36,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000185145.2_ASM18514v2_genomic.fna/markers.fasta)
[2024-01-24 13:47:36,253] [INFO] Task started: Blastn
[2024-01-24 13:47:36,254] [INFO] Running command: blastn -query GCF_000185145.2_ASM18514v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf62898c0-fd40-4b1f-891c-069ad97f0ae9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000185145.2_ASM18514v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:37,088] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:37,092] [INFO] Selected 26 target genomes.
[2024-01-24 13:47:37,092] [INFO] Target genome list was writen to GCF_000185145.2_ASM18514v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:37,158] [INFO] Task started: fastANI
[2024-01-24 13:47:37,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg5058c91d-e93c-4f24-bb1c-fa01f2780d60/GCF_000185145.2_ASM18514v2_genomic.fna.gz --refList GCF_000185145.2_ASM18514v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000185145.2_ASM18514v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:49,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:49,654] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:49,654] [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_000185145.2	s__Prevotella oralis	100.0	942	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.13	0.96	0.92	6	conclusive
GCF_000144405.1	s__Prevotella melaninogenica	79.3668	59	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_900637655.1	s__Prevotella oris	78.732	86	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000613785.1	s__Prevotella oulorum	78.3204	63	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	-
GCF_001553265.1	s__Prevotella sp001553265	78.2782	68	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.33	99.33	0.90	0.90	2	-
GCF_003043925.1	s__Prevotella sp003043925	78.1419	95	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000613405.1	s__Prevotella enoeca	77.4864	80	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.97	1.00	1.00	2	-
GCA_900316015.1	s__Prevotella sp900316015	77.4349	56	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.19	98.89	0.88	0.75	5	-
GCF_001275135.1	s__Prevotella rara	77.1359	67	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCF_000378085.1	s__Prevotella loescheii	76.767	63	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	-
GCA_900554695.1	s__Prevotella sp900554695	76.7665	54	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.88	0.84	0.83	3	-
GCA_902769705.1	s__Prevotella sp902769705	76.2239	52	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.53	0.84	0.80	3	-
GCA_905373605.1	s__Prevotella sp905373605	76.1542	51	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:49,656] [INFO] GTDB search result was written to GCF_000185145.2_ASM18514v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:49,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:49,661] [INFO] DFAST_QC result json was written to GCF_000185145.2_ASM18514v2_genomic.fna/dqc_result.json
[2024-01-24 13:47:49,662] [INFO] DFAST_QC completed!
[2024-01-24 13:47:49,662] [INFO] Total running time: 0h1m24s