[2023-06-13 16:35:29,108] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:35:29,113] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:35:29,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference
[2023-06-13 16:35:30,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:35:30,423] [INFO] Task started: Prodigal
[2023-06-13 16:35:30,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ad5d6e6-49cb-41a0-ba4f-e2a259915430/GCA_022769255.1_ASM2276925v1_genomic.fna.gz | prodigal -d GCA_022769255.1_ASM2276925v1_genomic.fna/cds.fna -a GCA_022769255.1_ASM2276925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:35:40,989] [INFO] Task succeeded: Prodigal
[2023-06-13 16:35:40,989] [INFO] Task started: HMMsearch
[2023-06-13 16:35:40,990] [INFO] Running command: hmmsearch --tblout GCA_022769255.1_ASM2276925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference/reference_markers.hmm GCA_022769255.1_ASM2276925v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:35:41,238] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:35:41,240] [INFO] Found 6/6 markers.
[2023-06-13 16:35:41,264] [INFO] Query marker FASTA was written to GCA_022769255.1_ASM2276925v1_genomic.fna/markers.fasta
[2023-06-13 16:35:41,264] [INFO] Task started: Blastn
[2023-06-13 16:35:41,264] [INFO] Running command: blastn -query GCA_022769255.1_ASM2276925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference/reference_markers.fasta -out GCA_022769255.1_ASM2276925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:35:41,883] [INFO] Task succeeded: Blastn
[2023-06-13 16:35:41,887] [INFO] Selected 31 target genomes.
[2023-06-13 16:35:41,887] [INFO] Target genome list was writen to GCA_022769255.1_ASM2276925v1_genomic.fna/target_genomes.txt
[2023-06-13 16:35:41,889] [INFO] Task started: fastANI
[2023-06-13 16:35:41,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ad5d6e6-49cb-41a0-ba4f-e2a259915430/GCA_022769255.1_ASM2276925v1_genomic.fna.gz --refList GCA_022769255.1_ASM2276925v1_genomic.fna/target_genomes.txt --output GCA_022769255.1_ASM2276925v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:35:57,378] [INFO] Task succeeded: fastANI
[2023-06-13 16:35:57,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:35:57,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:35:57,395] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:35:57,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 16:35:57,395] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.9331	92	591	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.8612	91	591	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.6778	61	591	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.6554	63	591	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.6397	78	591	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.5811	55	591	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.4925	56	591	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.4542	65	591	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.4217	64	591	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.3938	74	591	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.3081	72	591	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.2058	79	591	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.0283	52	591	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	75.7127	73	591	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	75.6926	72	591	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:35:57,397] [INFO] DFAST Taxonomy check result was written to GCA_022769255.1_ASM2276925v1_genomic.fna/tc_result.tsv
[2023-06-13 16:35:57,398] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:35:57,398] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:35:57,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference/checkm_data
[2023-06-13 16:35:57,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:35:57,425] [INFO] Task started: CheckM
[2023-06-13 16:35:57,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022769255.1_ASM2276925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022769255.1_ASM2276925v1_genomic.fna/checkm_input GCA_022769255.1_ASM2276925v1_genomic.fna/checkm_result
[2023-06-13 16:36:32,512] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:32,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:32,539] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:32,540] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:32,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022769255.1_ASM2276925v1_genomic.fna/markers.fasta)
[2023-06-13 16:36:32,541] [INFO] Task started: Blastn
[2023-06-13 16:36:32,541] [INFO] Running command: blastn -query GCA_022769255.1_ASM2276925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eee6fbb-bc73-4a4b-a18b-9e53a4bffedc/dqc_reference/reference_markers_gtdb.fasta -out GCA_022769255.1_ASM2276925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:33,401] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:33,407] [INFO] Selected 24 target genomes.
[2023-06-13 16:36:33,407] [INFO] Target genome list was writen to GCA_022769255.1_ASM2276925v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:33,415] [INFO] Task started: fastANI
[2023-06-13 16:36:33,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ad5d6e6-49cb-41a0-ba4f-e2a259915430/GCA_022769255.1_ASM2276925v1_genomic.fna.gz --refList GCA_022769255.1_ASM2276925v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022769255.1_ASM2276925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:44,411] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:44,433] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:36:44,433] [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_900547005.1	s__Prevotella sp900547005	96.5615	466	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.66	96.14	0.84	0.69	4	conclusive
GCA_900549175.1	s__Prevotella sp900549175	77.2206	95	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_900544495.1	s__Prevotella sp900544495	77.104	83	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_902780025.1	s__Prevotella sp902780025	76.9157	56	591	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	76.8161	95	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_013166545.1	s__Prevotella sp013166545	76.6972	77	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_900550035.1	s__Prevotella sp900550035	76.6543	81	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_900769055.1	s__Prevotella sp900769055	76.6229	80	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000191065.1	s__Prevotella multiformis	76.5811	55	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.87	0.89	0.89	2	-
GCA_905198745.1	s__Prevotella sp905198745	76.4426	59	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353555.1	s__Prevotella sp002353555	76.4268	77	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.57	0.79	0.77	3	-
GCA_900546575.1	s__Prevotella sp900546575	76.4048	74	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_902792685.1	s__Prevotella sp902792685	76.3818	67	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.79	96.68	0.73	0.71	4	-
GCF_000184945.1	s__Prevotella buccae	76.3391	74	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_017442765.1	s__Prevotella sp017442765	75.8198	53	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458125.1	s__Prevotella sp017458125	75.7357	66	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.42	97.42	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:44,435] [INFO] GTDB search result was written to GCA_022769255.1_ASM2276925v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:44,436] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:44,440] [INFO] DFAST_QC result json was written to GCA_022769255.1_ASM2276925v1_genomic.fna/dqc_result.json
[2023-06-13 16:36:44,440] [INFO] DFAST_QC completed!
[2023-06-13 16:36:44,440] [INFO] Total running time: 0h1m15s