[2024-01-24 12:45:09,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,083] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,084] [INFO] Running command: gunzip -c /var/lib/cwl/stgec8f73f0-747f-46f8-b213-36c648017b10/GCF_013166605.1_ASM1316660v1_genomic.fna.gz | prodigal -d GCF_013166605.1_ASM1316660v1_genomic.fna/cds.fna -a GCF_013166605.1_ASM1316660v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:31,394] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:31,394] [INFO] Task started: HMMsearch
[2024-01-24 12:45:31,394] [INFO] Running command: hmmsearch --tblout GCF_013166605.1_ASM1316660v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference/reference_markers.hmm GCF_013166605.1_ASM1316660v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:31,673] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:31,674] [INFO] Found 6/6 markers.
[2024-01-24 12:45:31,708] [INFO] Query marker FASTA was written to GCF_013166605.1_ASM1316660v1_genomic.fna/markers.fasta
[2024-01-24 12:45:31,708] [INFO] Task started: Blastn
[2024-01-24 12:45:31,708] [INFO] Running command: blastn -query GCF_013166605.1_ASM1316660v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference/reference_markers.fasta -out GCF_013166605.1_ASM1316660v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:32,281] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:32,285] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:32,286] [INFO] Target genome list was writen to GCF_013166605.1_ASM1316660v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:32,308] [INFO] Task started: fastANI
[2024-01-24 12:45:32,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8f73f0-747f-46f8-b213-36c648017b10/GCF_013166605.1_ASM1316660v1_genomic.fna.gz --refList GCF_013166605.1_ASM1316660v1_genomic.fna/target_genomes.txt --output GCF_013166605.1_ASM1316660v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:44,784] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:44,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:44,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:44,800] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:44,800] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:44,800] [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 muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	100.0	1103	1103	95	conclusive
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	80.6539	69	1103	95	below_threshold
Paraprevotella clara	strain=YIT 11840	GCA_000233955.1	454154	454154	type	True	79.1835	55	1103	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	78.5889	174	1103	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.3124	95	1103	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.172	78	1103	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.3731	54	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:44,802] [INFO] DFAST Taxonomy check result was written to GCF_013166605.1_ASM1316660v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:44,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:44,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:44,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference/checkm_data
[2024-01-24 12:45:44,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:44,837] [INFO] Task started: CheckM
[2024-01-24 12:45:44,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013166605.1_ASM1316660v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013166605.1_ASM1316660v1_genomic.fna/checkm_input GCF_013166605.1_ASM1316660v1_genomic.fna/checkm_result
[2024-01-24 12:46:38,732] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:38,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:38,753] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:38,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:38,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013166605.1_ASM1316660v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:38,754] [INFO] Task started: Blastn
[2024-01-24 12:46:38,754] [INFO] Running command: blastn -query GCF_013166605.1_ASM1316660v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e7338e-17e4-4a38-88ab-4233a75b908e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013166605.1_ASM1316660v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:39,560] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:39,564] [INFO] Selected 22 target genomes.
[2024-01-24 12:46:39,564] [INFO] Target genome list was writen to GCF_013166605.1_ASM1316660v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:39,632] [INFO] Task started: fastANI
[2024-01-24 12:46:39,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8f73f0-747f-46f8-b213-36c648017b10/GCF_013166605.1_ASM1316660v1_genomic.fna.gz --refList GCF_013166605.1_ASM1316660v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013166605.1_ASM1316660v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:51,823] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:51,839] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:51,840] [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_013166605.1	s__Prevotella sp013166605	100.0	1103	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.90	99.90	0.99	0.99	2	conclusive
GCF_003977605.1	s__Prevotella koreensis	80.6539	69	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000233955.1	s__Paraprevotella clara	79.1835	55	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	97.73	97.27	0.87	0.80	9	-
GCF_013166545.1	s__Prevotella sp013166545	78.6839	179	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCF_002933775.1	s__Prevotella sp002933775	78.4436	153	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	97.52	0.85	0.83	11	-
GCA_017623155.1	s__Prevotella sp017623155	77.7783	127	1103	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	77.3788	91	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	-
GCF_000834015.1	s__Prevotella pectinovora	77.1849	80	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_017483185.1	s__Prevotella sp017483185	77.0924	105	1103	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	76.9222	135	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_000433175.1	s__Prevotella sp000433175	76.8096	63	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCF_016899955.1	s__Prevotella sp900540415	76.6722	105	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCF_002251245.1	s__Prevotella sp002251245	76.5985	99	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.53	98.53	0.91	0.91	2	-
GCA_016291595.1	s__Prevotella sp016291595	76.5863	64	1103	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	76.5708	127	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_900548745.1	s__Prevotella sp900548745	76.3345	69	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.94	97.91	0.83	0.71	3	-
GCA_900315455.1	s__Prevotella sp900315455	75.6727	63	1103	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:51,841] [INFO] GTDB search result was written to GCF_013166605.1_ASM1316660v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:51,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:51,845] [INFO] DFAST_QC result json was written to GCF_013166605.1_ASM1316660v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:51,845] [INFO] DFAST_QC completed!
[2024-01-24 12:46:51,845] [INFO] Total running time: 0h1m42s