[2023-06-13 14:27:52,308] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:27:52,313] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:27:52,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference
[2023-06-13 14:27:53,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:27:53,612] [INFO] Task started: Prodigal
[2023-06-13 14:27:53,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg25b76729-c0e4-43e2-a37a-8c37ae0deb5a/GCA_022772365.1_ASM2277236v1_genomic.fna.gz | prodigal -d GCA_022772365.1_ASM2277236v1_genomic.fna/cds.fna -a GCA_022772365.1_ASM2277236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:28:07,901] [INFO] Task succeeded: Prodigal
[2023-06-13 14:28:07,902] [INFO] Task started: HMMsearch
[2023-06-13 14:28:07,902] [INFO] Running command: hmmsearch --tblout GCA_022772365.1_ASM2277236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference/reference_markers.hmm GCA_022772365.1_ASM2277236v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:28:08,139] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:28:08,141] [INFO] Found 6/6 markers.
[2023-06-13 14:28:08,191] [INFO] Query marker FASTA was written to GCA_022772365.1_ASM2277236v1_genomic.fna/markers.fasta
[2023-06-13 14:28:08,191] [INFO] Task started: Blastn
[2023-06-13 14:28:08,192] [INFO] Running command: blastn -query GCA_022772365.1_ASM2277236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference/reference_markers.fasta -out GCA_022772365.1_ASM2277236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:28:08,801] [INFO] Task succeeded: Blastn
[2023-06-13 14:28:08,805] [INFO] Selected 27 target genomes.
[2023-06-13 14:28:08,806] [INFO] Target genome list was writen to GCA_022772365.1_ASM2277236v1_genomic.fna/target_genomes.txt
[2023-06-13 14:28:08,808] [INFO] Task started: fastANI
[2023-06-13 14:28:08,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg25b76729-c0e4-43e2-a37a-8c37ae0deb5a/GCA_022772365.1_ASM2277236v1_genomic.fna.gz --refList GCA_022772365.1_ASM2277236v1_genomic.fna/target_genomes.txt --output GCA_022772365.1_ASM2277236v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:28:22,150] [INFO] Task succeeded: fastANI
[2023-06-13 14:28:22,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:28:22,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:28:22,171] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:28:22,171] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:28:22,172] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.7164	197	735	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.7164	141	735	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.5246	123	735	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.3215	53	735	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.2386	151	735	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.0001	90	735	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.9317	91	735	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.9265	91	735	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.8785	90	735	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.8001	100	735	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.6608	78	735	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.6025	93	735	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.575	87	735	95	below_threshold
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	76.3442	53	735	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.2406	67	735	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:28:22,174] [INFO] DFAST Taxonomy check result was written to GCA_022772365.1_ASM2277236v1_genomic.fna/tc_result.tsv
[2023-06-13 14:28:22,174] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:28:22,175] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:28:22,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference/checkm_data
[2023-06-13 14:28:22,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:28:22,203] [INFO] Task started: CheckM
[2023-06-13 14:28:22,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022772365.1_ASM2277236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022772365.1_ASM2277236v1_genomic.fna/checkm_input GCA_022772365.1_ASM2277236v1_genomic.fna/checkm_result
[2023-06-13 14:29:05,024] [INFO] Task succeeded: CheckM
[2023-06-13 14:29:05,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:29:05,045] [INFO] ===== Completeness check finished =====
[2023-06-13 14:29:05,046] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:29:05,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022772365.1_ASM2277236v1_genomic.fna/markers.fasta)
[2023-06-13 14:29:05,046] [INFO] Task started: Blastn
[2023-06-13 14:29:05,046] [INFO] Running command: blastn -query GCA_022772365.1_ASM2277236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452b2b7a-7cf9-4293-b16b-b40460a2d89d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022772365.1_ASM2277236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:29:05,921] [INFO] Task succeeded: Blastn
[2023-06-13 14:29:05,925] [INFO] Selected 20 target genomes.
[2023-06-13 14:29:05,926] [INFO] Target genome list was writen to GCA_022772365.1_ASM2277236v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:29:05,927] [INFO] Task started: fastANI
[2023-06-13 14:29:05,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg25b76729-c0e4-43e2-a37a-8c37ae0deb5a/GCA_022772365.1_ASM2277236v1_genomic.fna.gz --refList GCA_022772365.1_ASM2277236v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022772365.1_ASM2277236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:29:14,891] [INFO] Task succeeded: fastANI
[2023-06-13 14:29:14,910] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:29:14,910] [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_900543975.1	s__Prevotella sp900543975	80.7468	351	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_900552675.1	s__Prevotella sp900552675	78.91	185	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	95.81	0.80	0.75	5	-
GCF_000235885.1	s__Prevotella stercorea	78.7504	196	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCF_002265625.1	s__Prevotella sp002265625	78.6425	190	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900550035.1	s__Prevotella sp900550035	78.5432	197	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_002490315.1	s__Prevotella sp002490315	78.5345	147	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019052365.1	s__Prevotella sp000434975	78.5109	198	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_900553595.1	s__Prevotella sp900553595	78.2773	170	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	97.92	0.92	0.85	3	-
GCA_900553155.1	s__Prevotella sp900553155	78.0111	135	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900546575.1	s__Prevotella sp900546575	77.9894	203	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCF_900290275.1	s__Prevotella sp900290275	77.9257	146	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
GCA_905216025.1	s__Prevotella sp905216025	77.4899	139	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_905198745.1	s__Prevotella sp905198745	77.0065	120	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549175.1	s__Prevotella sp900549175	76.9323	136	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_902801375.1	s__Prevotella sp902801375	76.9259	86	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
GCF_001275135.1	s__Prevotella rara	76.9212	112	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_900769055.1	s__Prevotella sp900769055	76.9037	96	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166545.1	s__Prevotella sp013166545	76.8801	91	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_900315095.1	s__Prevotella sp900315095	76.8669	91	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
GCA_017442765.1	s__Prevotella sp017442765	76.5205	93	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:29:14,913] [INFO] GTDB search result was written to GCA_022772365.1_ASM2277236v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:29:14,913] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:29:14,917] [INFO] DFAST_QC result json was written to GCA_022772365.1_ASM2277236v1_genomic.fna/dqc_result.json
[2023-06-13 14:29:14,918] [INFO] DFAST_QC completed!
[2023-06-13 14:29:14,918] [INFO] Total running time: 0h1m23s