[2023-06-28 23:39:18,589] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:39:18,595] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:39:18,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference
[2023-06-28 23:39:19,920] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:39:19,921] [INFO] Task started: Prodigal
[2023-06-28 23:39:19,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf4ae7c2-1e76-4518-85aa-3b637569cbf5/GCA_017620635.1_ASM1762063v1_genomic.fna.gz | prodigal -d GCA_017620635.1_ASM1762063v1_genomic.fna/cds.fna -a GCA_017620635.1_ASM1762063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:39:31,819] [INFO] Task succeeded: Prodigal
[2023-06-28 23:39:31,819] [INFO] Task started: HMMsearch
[2023-06-28 23:39:31,819] [INFO] Running command: hmmsearch --tblout GCA_017620635.1_ASM1762063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference/reference_markers.hmm GCA_017620635.1_ASM1762063v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:39:32,047] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:39:32,049] [INFO] Found 6/6 markers.
[2023-06-28 23:39:32,079] [INFO] Query marker FASTA was written to GCA_017620635.1_ASM1762063v1_genomic.fna/markers.fasta
[2023-06-28 23:39:32,080] [INFO] Task started: Blastn
[2023-06-28 23:39:32,080] [INFO] Running command: blastn -query GCA_017620635.1_ASM1762063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference/reference_markers.fasta -out GCA_017620635.1_ASM1762063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:39:32,836] [INFO] Task succeeded: Blastn
[2023-06-28 23:39:32,841] [INFO] Selected 24 target genomes.
[2023-06-28 23:39:32,841] [INFO] Target genome list was writen to GCA_017620635.1_ASM1762063v1_genomic.fna/target_genomes.txt
[2023-06-28 23:39:32,845] [INFO] Task started: fastANI
[2023-06-28 23:39:32,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf4ae7c2-1e76-4518-85aa-3b637569cbf5/GCA_017620635.1_ASM1762063v1_genomic.fna.gz --refList GCA_017620635.1_ASM1762063v1_genomic.fna/target_genomes.txt --output GCA_017620635.1_ASM1762063v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:39:50,628] [INFO] Task succeeded: fastANI
[2023-06-28 23:39:50,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:39:50,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:39:50,645] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:39:50,646] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:39:50,646] [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
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.0539	75	699	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.7603	82	699	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.7288	82	699	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.7091	85	699	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.5583	76	699	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.3578	72	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:39:50,648] [INFO] DFAST Taxonomy check result was written to GCA_017620635.1_ASM1762063v1_genomic.fna/tc_result.tsv
[2023-06-28 23:39:50,649] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:39:50,649] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:39:50,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference/checkm_data
[2023-06-28 23:39:50,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:39:50,680] [INFO] Task started: CheckM
[2023-06-28 23:39:50,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017620635.1_ASM1762063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017620635.1_ASM1762063v1_genomic.fna/checkm_input GCA_017620635.1_ASM1762063v1_genomic.fna/checkm_result
[2023-06-28 23:40:27,813] [INFO] Task succeeded: CheckM
[2023-06-28 23:40:27,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:40:27,835] [INFO] ===== Completeness check finished =====
[2023-06-28 23:40:27,836] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:40:27,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017620635.1_ASM1762063v1_genomic.fna/markers.fasta)
[2023-06-28 23:40:27,836] [INFO] Task started: Blastn
[2023-06-28 23:40:27,837] [INFO] Running command: blastn -query GCA_017620635.1_ASM1762063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91239b9e-a2d0-4eff-ab97-968a6bce8742/dqc_reference/reference_markers_gtdb.fasta -out GCA_017620635.1_ASM1762063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:28,764] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:28,769] [INFO] Selected 15 target genomes.
[2023-06-28 23:40:28,769] [INFO] Target genome list was writen to GCA_017620635.1_ASM1762063v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:40:28,807] [INFO] Task started: fastANI
[2023-06-28 23:40:28,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf4ae7c2-1e76-4518-85aa-3b637569cbf5/GCA_017620635.1_ASM1762063v1_genomic.fna.gz --refList GCA_017620635.1_ASM1762063v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017620635.1_ASM1762063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:40:35,854] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:35,870] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:40:35,870] [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_017620635.1	s__CAG-873 sp017620635	100.0	694	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009775195.1	s__CAG-873 sp009775195	79.2698	267	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.01	95.47	0.84	0.74	3	-
GCA_002491245.1	s__CAG-873 sp002491245	79.1214	274	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.67	97.75	0.93	0.87	9	-
GCA_910579995.1	s__CAG-873 sp009775135	78.9834	283	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.86	99.86	0.96	0.96	2	-
GCA_001689415.1	s__CAG-873 sp001689415	78.6083	236	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.88	97.88	0.88	0.88	2	-
GCA_900759845.1	s__CAG-873 sp900759845	78.0731	184	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548975.1	s__CAG-873 sp900548975	78.0254	179	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.98	99.96	0.94	0.89	3	-
GCA_002493945.1	s__CAG-873 sp002493945	77.839	174	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.61	97.51	0.95	0.88	8	-
GCA_910578035.1	s__CAG-873 sp910578035	77.6943	120	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800735.1	s__CAG-873 sp014800735	77.6448	144	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.24	97.04	0.84	0.82	3	-
GCA_910586595.1	s__CAG-873 sp910586595	77.5803	135	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541865.1	s__CAG-873 sp900541865	77.5641	110	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937625.1	s__CAG-873 sp017937625	77.5096	158	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555715.1	s__CAG-873 sp900555715	77.4606	131	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.36	96.57	0.81	0.79	3	-
GCA_905202215.1	s__CAG-873 sp905202215	77.4591	146	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.54	98.54	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-28 23:40:35,872] [INFO] GTDB search result was written to GCA_017620635.1_ASM1762063v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:40:35,873] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:40:35,876] [INFO] DFAST_QC result json was written to GCA_017620635.1_ASM1762063v1_genomic.fna/dqc_result.json
[2023-06-28 23:40:35,877] [INFO] DFAST_QC completed!
[2023-06-28 23:40:35,877] [INFO] Total running time: 0h1m17s