[2023-06-13 13:25:14,230] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:25:14,234] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:25:14,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference
[2023-06-13 13:25:15,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:25:15,389] [INFO] Task started: Prodigal
[2023-06-13 13:25:15,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg7be4c5bc-2827-49c2-b370-c7ab645e287e/GCA_022773545.1_ASM2277354v1_genomic.fna.gz | prodigal -d GCA_022773545.1_ASM2277354v1_genomic.fna/cds.fna -a GCA_022773545.1_ASM2277354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:25:34,230] [INFO] Task succeeded: Prodigal
[2023-06-13 13:25:34,231] [INFO] Task started: HMMsearch
[2023-06-13 13:25:34,231] [INFO] Running command: hmmsearch --tblout GCA_022773545.1_ASM2277354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference/reference_markers.hmm GCA_022773545.1_ASM2277354v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:25:34,434] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:25:34,435] [INFO] Found 6/6 markers.
[2023-06-13 13:25:34,467] [INFO] Query marker FASTA was written to GCA_022773545.1_ASM2277354v1_genomic.fna/markers.fasta
[2023-06-13 13:25:34,467] [INFO] Task started: Blastn
[2023-06-13 13:25:34,467] [INFO] Running command: blastn -query GCA_022773545.1_ASM2277354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference/reference_markers.fasta -out GCA_022773545.1_ASM2277354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:25:35,030] [INFO] Task succeeded: Blastn
[2023-06-13 13:25:35,034] [INFO] Selected 30 target genomes.
[2023-06-13 13:25:35,034] [INFO] Target genome list was writen to GCA_022773545.1_ASM2277354v1_genomic.fna/target_genomes.txt
[2023-06-13 13:25:35,037] [INFO] Task started: fastANI
[2023-06-13 13:25:35,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg7be4c5bc-2827-49c2-b370-c7ab645e287e/GCA_022773545.1_ASM2277354v1_genomic.fna.gz --refList GCA_022773545.1_ASM2277354v1_genomic.fna/target_genomes.txt --output GCA_022773545.1_ASM2277354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:25:50,144] [INFO] Task succeeded: fastANI
[2023-06-13 13:25:50,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:25:50,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:25:50,159] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:25:50,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:25:50,159] [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 copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.5854	128	1030	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	78.5725	135	1030	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	78.548	132	1030	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.7597	129	1030	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.2891	109	1030	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.0805	122	1030	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.0411	124	1030	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.986	114	1030	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.9218	59	1030	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.9079	61	1030	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.7331	86	1030	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.7215	100	1030	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.5879	51	1030	95	below_threshold
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	76.5058	52	1030	95	below_threshold
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	76.4117	51	1030	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.1196	56	1030	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.0924	57	1030	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:25:50,161] [INFO] DFAST Taxonomy check result was written to GCA_022773545.1_ASM2277354v1_genomic.fna/tc_result.tsv
[2023-06-13 13:25:50,161] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:25:50,162] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:25:50,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference/checkm_data
[2023-06-13 13:25:50,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:25:50,196] [INFO] Task started: CheckM
[2023-06-13 13:25:50,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022773545.1_ASM2277354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022773545.1_ASM2277354v1_genomic.fna/checkm_input GCA_022773545.1_ASM2277354v1_genomic.fna/checkm_result
[2023-06-13 13:26:44,292] [INFO] Task succeeded: CheckM
[2023-06-13 13:26:44,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 5.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 13:26:44,320] [INFO] ===== Completeness check finished =====
[2023-06-13 13:26:44,320] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:26:44,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022773545.1_ASM2277354v1_genomic.fna/markers.fasta)
[2023-06-13 13:26:44,321] [INFO] Task started: Blastn
[2023-06-13 13:26:44,321] [INFO] Running command: blastn -query GCA_022773545.1_ASM2277354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f8fca6-e8d1-4511-bcc9-8580ceaf8c74/dqc_reference/reference_markers_gtdb.fasta -out GCA_022773545.1_ASM2277354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:26:45,191] [INFO] Task succeeded: Blastn
[2023-06-13 13:26:45,195] [INFO] Selected 28 target genomes.
[2023-06-13 13:26:45,195] [INFO] Target genome list was writen to GCA_022773545.1_ASM2277354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:26:45,200] [INFO] Task started: fastANI
[2023-06-13 13:26:45,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg7be4c5bc-2827-49c2-b370-c7ab645e287e/GCA_022773545.1_ASM2277354v1_genomic.fna.gz --refList GCA_022773545.1_ASM2277354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022773545.1_ASM2277354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:26:59,047] [INFO] Task succeeded: fastANI
[2023-06-13 13:26:59,068] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:26:59,068] [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_002251435.1	s__Prevotella sp002251435	83.2541	390	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251245.1	s__Prevotella sp002251245	81.724	369	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.53	98.53	0.91	0.91	2	-
GCA_900557255.1	s__Prevotella sp900557255	78.5752	84	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157935.1	s__Prevotella copri	78.5751	136	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_015074785.1	s__Prevotella sp015074785	78.1786	127	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_900543975.1	s__Prevotella sp900543975	77.9025	105	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCF_019127135.1	s__Prevotella sp900551275	77.8585	135	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_016302965.1	s__Prevotella sp016302965	77.836	188	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410365.1	s__Prevotella sp017410365	77.5427	126	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	-
GCA_018385335.1	s__Prevotella sp018385335	77.4885	178	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557035.1	s__Prevotella sp900557035	77.3158	83	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCF_002224675.1	s__Prevotella copri_A	77.3138	146	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_902776195.1	s__Prevotella sp902776195	77.3016	110	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.27	97.27	0.76	0.76	2	-
GCF_009494395.1	s__Prevotella sp900546535	77.1307	135	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCF_009495355.1	s__Prevotella sp900313215	77.087	125	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	-
GCA_002314055.1	s__Prevotella sp002314055	76.9688	121	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.98	0.90	0.84	9	-
GCA_002350805.1	s__Prevotella sp002350805	76.9628	102	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.30	97.51	0.83	0.79	8	-
GCA_017412705.1	s__Prevotella sp017412705	76.9239	110	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216025.1	s__Prevotella sp905216025	76.8031	142	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_902784615.1	s__Prevotella sp902784615	76.801	117	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166605.1	s__Prevotella sp013166605	76.7331	86	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.90	99.90	0.99	0.99	2	-
GCA_017965475.1	s__Prevotella sp017965475	76.7321	94	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318395.1	s__Prevotella sp900318395	76.7021	127	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.69	96.89	0.88	0.81	6	-
GCF_016899955.1	s__Prevotella sp900540415	76.6301	126	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_902771155.1	s__Prevotella sp902771155	76.602	109	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933775.1	s__Prevotella sp002933775	76.5165	98	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	97.52	0.85	0.83	11	-
GCA_002305505.1	s__Prevotella sp002305505	76.5145	86	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548275.1	s__Prevotella sp017548275	76.4689	94	1030	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 13:26:59,071] [INFO] GTDB search result was written to GCA_022773545.1_ASM2277354v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:26:59,071] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:26:59,076] [INFO] DFAST_QC result json was written to GCA_022773545.1_ASM2277354v1_genomic.fna/dqc_result.json
[2023-06-13 13:26:59,076] [INFO] DFAST_QC completed!
[2023-06-13 13:26:59,076] [INFO] Total running time: 0h1m45s