[2024-01-24 15:10:41,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference
[2024-01-24 15:10:42,504] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,508] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg9abe2c9e-ae9d-4954-b6ce-74c98d148dbe/GCF_013166575.1_ASM1316657v1_genomic.fna.gz | prodigal -d GCF_013166575.1_ASM1316657v1_genomic.fna/cds.fna -a GCF_013166575.1_ASM1316657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:03,945] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:03,945] [INFO] Task started: HMMsearch
[2024-01-24 15:11:03,945] [INFO] Running command: hmmsearch --tblout GCF_013166575.1_ASM1316657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference/reference_markers.hmm GCF_013166575.1_ASM1316657v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:04,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:04,286] [INFO] Found 6/6 markers.
[2024-01-24 15:11:04,332] [INFO] Query marker FASTA was written to GCF_013166575.1_ASM1316657v1_genomic.fna/markers.fasta
[2024-01-24 15:11:04,333] [INFO] Task started: Blastn
[2024-01-24 15:11:04,333] [INFO] Running command: blastn -query GCF_013166575.1_ASM1316657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference/reference_markers.fasta -out GCF_013166575.1_ASM1316657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:05,078] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:05,084] [INFO] Selected 20 target genomes.
[2024-01-24 15:11:05,084] [INFO] Target genome list was writen to GCF_013166575.1_ASM1316657v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:05,095] [INFO] Task started: fastANI
[2024-01-24 15:11:05,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg9abe2c9e-ae9d-4954-b6ce-74c98d148dbe/GCF_013166575.1_ASM1316657v1_genomic.fna.gz --refList GCF_013166575.1_ASM1316657v1_genomic.fna/target_genomes.txt --output GCF_013166575.1_ASM1316657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:17,790] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:17,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:17,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:17,802] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:17,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:17,802] [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
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	100.0	1137	1139	95	conclusive
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	83.3975	56	1139	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	79.8061	78	1139	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	79.774	87	1139	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	78.5018	174	1139	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.5062	65	1139	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	77.4276	59	1139	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.2023	112	1139	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.0348	63	1139	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.9841	80	1139	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.8464	59	1139	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.8221	66	1139	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.7254	109	1139	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.6287	78	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:17,804] [INFO] DFAST Taxonomy check result was written to GCF_013166575.1_ASM1316657v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:17,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:17,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:17,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference/checkm_data
[2024-01-24 15:11:17,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:17,845] [INFO] Task started: CheckM
[2024-01-24 15:11:17,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013166575.1_ASM1316657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013166575.1_ASM1316657v1_genomic.fna/checkm_input GCF_013166575.1_ASM1316657v1_genomic.fna/checkm_result
[2024-01-24 15:12:19,044] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:19,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:19,065] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:19,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:19,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013166575.1_ASM1316657v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:19,066] [INFO] Task started: Blastn
[2024-01-24 15:12:19,066] [INFO] Running command: blastn -query GCF_013166575.1_ASM1316657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bda77b6-4704-4eb0-a0bb-9b38d0e7d23e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013166575.1_ASM1316657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:20,016] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:20,021] [INFO] Selected 14 target genomes.
[2024-01-24 15:12:20,021] [INFO] Target genome list was writen to GCF_013166575.1_ASM1316657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:20,032] [INFO] Task started: fastANI
[2024-01-24 15:12:20,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg9abe2c9e-ae9d-4954-b6ce-74c98d148dbe/GCF_013166575.1_ASM1316657v1_genomic.fna.gz --refList GCF_013166575.1_ASM1316657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013166575.1_ASM1316657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:28,638] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:28,653] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:28,653] [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_013166545.1	s__Prevotella sp013166545	99.8777	1102	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	conclusive
GCA_900549175.1	s__Prevotella sp900549175	81.1784	550	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_017483185.1	s__Prevotella sp017483185	79.1383	273	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553965.1	s__Prevotella sp900553965	78.5055	253	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.57	97.60	0.86	0.85	3	-
GCA_905216025.1	s__Prevotella sp905216025	78.3767	311	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_017623155.1	s__Prevotella sp017623155	78.1367	224	1139	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	78.1335	211	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	97.52	0.85	0.83	11	-
GCA_900545525.1	s__Prevotella sp900545525	78.0998	132	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCF_016899955.1	s__Prevotella sp900540415	77.2344	197	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_017410365.1	s__Prevotella sp017410365	77.0655	128	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	-
GCA_002394385.1	s__Prevotella sp002394385	76.8221	120	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_900772835.1	s__Prevotella sp900772835	76.4764	88	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315835.1	s__Prevotella sp900315835	76.2408	69	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCA_905198745.1	s__Prevotella sp905198745	76.2121	92	1139	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 15:12:28,655] [INFO] GTDB search result was written to GCF_013166575.1_ASM1316657v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:28,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:28,660] [INFO] DFAST_QC result json was written to GCF_013166575.1_ASM1316657v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:28,660] [INFO] DFAST_QC completed!
[2024-01-24 15:12:28,660] [INFO] Total running time: 0h1m48s