[2023-06-29 15:26:57,790] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:26:57,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:26:57,793] [INFO] DQC Reference Directory: /var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference
[2023-06-29 15:26:58,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:26:58,966] [INFO] Task started: Prodigal
[2023-06-29 15:26:58,966] [INFO] Running command: gunzip -c /var/lib/cwl/stgb39f7c38-ba95-4747-82ce-c587c440d7b6/GCA_910588475.1_MGBC162466_genomic.fna.gz | prodigal -d GCA_910588475.1_MGBC162466_genomic.fna/cds.fna -a GCA_910588475.1_MGBC162466_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:27:13,739] [INFO] Task succeeded: Prodigal
[2023-06-29 15:27:13,740] [INFO] Task started: HMMsearch
[2023-06-29 15:27:13,740] [INFO] Running command: hmmsearch --tblout GCA_910588475.1_MGBC162466_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference/reference_markers.hmm GCA_910588475.1_MGBC162466_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:27:14,038] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:27:14,040] [INFO] Found 6/6 markers.
[2023-06-29 15:27:14,076] [INFO] Query marker FASTA was written to GCA_910588475.1_MGBC162466_genomic.fna/markers.fasta
[2023-06-29 15:27:14,076] [INFO] Task started: Blastn
[2023-06-29 15:27:14,076] [INFO] Running command: blastn -query GCA_910588475.1_MGBC162466_genomic.fna/markers.fasta -db /var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference/reference_markers.fasta -out GCA_910588475.1_MGBC162466_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:27:14,806] [INFO] Task succeeded: Blastn
[2023-06-29 15:27:14,811] [INFO] Selected 20 target genomes.
[2023-06-29 15:27:14,812] [INFO] Target genome list was writen to GCA_910588475.1_MGBC162466_genomic.fna/target_genomes.txt
[2023-06-29 15:27:14,813] [INFO] Task started: fastANI
[2023-06-29 15:27:14,813] [INFO] Running command: fastANI --query /var/lib/cwl/stgb39f7c38-ba95-4747-82ce-c587c440d7b6/GCA_910588475.1_MGBC162466_genomic.fna.gz --refList GCA_910588475.1_MGBC162466_genomic.fna/target_genomes.txt --output GCA_910588475.1_MGBC162466_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:27:28,009] [INFO] Task succeeded: fastANI
[2023-06-29 15:27:28,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:27:28,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:27:28,024] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 15:27:28,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 15:27:28,025] [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
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	99.7273	877	915	95	conclusive
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.912	210	915	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.4515	145	915	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.4091	147	915	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.0136	91	915	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.9117	85	915	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	76.7031	68	915	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:27:28,027] [INFO] DFAST Taxonomy check result was written to GCA_910588475.1_MGBC162466_genomic.fna/tc_result.tsv
[2023-06-29 15:27:28,028] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:27:28,028] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:27:28,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference/checkm_data
[2023-06-29 15:27:28,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:27:28,063] [INFO] Task started: CheckM
[2023-06-29 15:27:28,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910588475.1_MGBC162466_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910588475.1_MGBC162466_genomic.fna/checkm_input GCA_910588475.1_MGBC162466_genomic.fna/checkm_result
[2023-06-29 15:28:13,116] [INFO] Task succeeded: CheckM
[2023-06-29 15:28:13,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:28:13,139] [INFO] ===== Completeness check finished =====
[2023-06-29 15:28:13,140] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:28:13,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910588475.1_MGBC162466_genomic.fna/markers.fasta)
[2023-06-29 15:28:13,140] [INFO] Task started: Blastn
[2023-06-29 15:28:13,141] [INFO] Running command: blastn -query GCA_910588475.1_MGBC162466_genomic.fna/markers.fasta -db /var/lib/cwl/stga1e0d7cd-8778-4e86-8848-21afa6c7fef4/dqc_reference/reference_markers_gtdb.fasta -out GCA_910588475.1_MGBC162466_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:28:13,995] [INFO] Task succeeded: Blastn
[2023-06-29 15:28:14,000] [INFO] Selected 12 target genomes.
[2023-06-29 15:28:14,001] [INFO] Target genome list was writen to GCA_910588475.1_MGBC162466_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:28:14,002] [INFO] Task started: fastANI
[2023-06-29 15:28:14,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgb39f7c38-ba95-4747-82ce-c587c440d7b6/GCA_910588475.1_MGBC162466_genomic.fna.gz --refList GCA_910588475.1_MGBC162466_genomic.fna/target_genomes_gtdb.txt --output GCA_910588475.1_MGBC162466_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:28:20,784] [INFO] Task succeeded: fastANI
[2023-06-29 15:28:20,818] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:28:20,819] [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_008728965.1	s__Muribaculum faecis	99.7273	877	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.62	99.32	0.94	0.91	9	conclusive
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	86.4111	714	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_009775095.1	s__Muribaculum sp009775095	86.1761	751	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCF_004570975.1	s__Muribaculum sp001701195	78.0451	215	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.86	97.86	0.92	0.92	2	-
GCA_910578835.1	s__Muribaculum sp910578835	77.9192	205	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003150235.1	s__Muribaculum sp003150235	77.785	205	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	-
GCA_910587665.1	s__Muribaculum sp910587665	77.7784	213	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001701065.1	s__Muribaculum sp001701065	77.35	113	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578785.1	s__Muribaculum sp910578785	77.1702	154	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801235.1	s__Muribaculum sp014801235	76.9304	80	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586975.1	s__CAG-873 sp910586975	76.5667	50	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:28:20,820] [INFO] GTDB search result was written to GCA_910588475.1_MGBC162466_genomic.fna/result_gtdb.tsv
[2023-06-29 15:28:20,821] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:28:20,824] [INFO] DFAST_QC result json was written to GCA_910588475.1_MGBC162466_genomic.fna/dqc_result.json
[2023-06-29 15:28:20,824] [INFO] DFAST_QC completed!
[2023-06-29 15:28:20,824] [INFO] Total running time: 0h1m23s