[2023-06-19 03:26:06,349] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:26:06,351] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:26:06,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference
[2023-06-19 03:26:07,610] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:26:07,611] [INFO] Task started: Prodigal
[2023-06-19 03:26:07,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bce8079-0879-4bef-a3c1-f2b2363b9fa7/GCA_014869835.1_ASM1486983v1_genomic.fna.gz | prodigal -d GCA_014869835.1_ASM1486983v1_genomic.fna/cds.fna -a GCA_014869835.1_ASM1486983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:26:12,564] [INFO] Task succeeded: Prodigal
[2023-06-19 03:26:12,564] [INFO] Task started: HMMsearch
[2023-06-19 03:26:12,564] [INFO] Running command: hmmsearch --tblout GCA_014869835.1_ASM1486983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference/reference_markers.hmm GCA_014869835.1_ASM1486983v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:26:12,806] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:26:12,807] [INFO] Found 6/6 markers.
[2023-06-19 03:26:12,840] [INFO] Query marker FASTA was written to GCA_014869835.1_ASM1486983v1_genomic.fna/markers.fasta
[2023-06-19 03:26:12,841] [INFO] Task started: Blastn
[2023-06-19 03:26:12,841] [INFO] Running command: blastn -query GCA_014869835.1_ASM1486983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference/reference_markers.fasta -out GCA_014869835.1_ASM1486983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:26:13,575] [INFO] Task succeeded: Blastn
[2023-06-19 03:26:13,579] [INFO] Selected 25 target genomes.
[2023-06-19 03:26:13,580] [INFO] Target genome list was writen to GCA_014869835.1_ASM1486983v1_genomic.fna/target_genomes.txt
[2023-06-19 03:26:13,583] [INFO] Task started: fastANI
[2023-06-19 03:26:13,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bce8079-0879-4bef-a3c1-f2b2363b9fa7/GCA_014869835.1_ASM1486983v1_genomic.fna.gz --refList GCA_014869835.1_ASM1486983v1_genomic.fna/target_genomes.txt --output GCA_014869835.1_ASM1486983v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:26:32,556] [INFO] Task succeeded: fastANI
[2023-06-19 03:26:32,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:26:32,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:26:32,565] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:26:32,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:26:32,566] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.0835	61	511	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.0695	67	511	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.9662	66	511	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.8267	58	511	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.7809	59	511	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.543	65	511	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.1183	65	511	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:26:32,574] [INFO] DFAST Taxonomy check result was written to GCA_014869835.1_ASM1486983v1_genomic.fna/tc_result.tsv
[2023-06-19 03:26:32,575] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:26:32,575] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:26:32,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference/checkm_data
[2023-06-19 03:26:32,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:26:32,609] [INFO] Task started: CheckM
[2023-06-19 03:26:32,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014869835.1_ASM1486983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014869835.1_ASM1486983v1_genomic.fna/checkm_input GCA_014869835.1_ASM1486983v1_genomic.fna/checkm_result
[2023-06-19 03:26:54,242] [INFO] Task succeeded: CheckM
[2023-06-19 03:26:54,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:26:54,267] [INFO] ===== Completeness check finished =====
[2023-06-19 03:26:54,267] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:26:54,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014869835.1_ASM1486983v1_genomic.fna/markers.fasta)
[2023-06-19 03:26:54,268] [INFO] Task started: Blastn
[2023-06-19 03:26:54,268] [INFO] Running command: blastn -query GCA_014869835.1_ASM1486983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f3de93d-5acb-4b6f-87c1-4df38978435d/dqc_reference/reference_markers_gtdb.fasta -out GCA_014869835.1_ASM1486983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:26:55,585] [INFO] Task succeeded: Blastn
[2023-06-19 03:26:55,590] [INFO] Selected 6 target genomes.
[2023-06-19 03:26:55,590] [INFO] Target genome list was writen to GCA_014869835.1_ASM1486983v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:26:55,592] [INFO] Task started: fastANI
[2023-06-19 03:26:55,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bce8079-0879-4bef-a3c1-f2b2363b9fa7/GCA_014869835.1_ASM1486983v1_genomic.fna.gz --refList GCA_014869835.1_ASM1486983v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014869835.1_ASM1486983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:26:58,323] [INFO] Task succeeded: fastANI
[2023-06-19 03:26:58,335] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:26:58,336] [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_000432375.1	s__CAG-103 sp000432375	97.8916	431	511	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	conclusive
GCA_900317855.1	s__CAG-103 sp900317855	94.3175	450	511	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_900757655.1	s__CAG-103 sp900757655	93.6905	434	511	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	-
GCA_900543625.1	s__CAG-103 sp900543625	91.0327	456	511	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
GCA_004556965.1	s__CAG-103 sp004556965	81.2439	311	511	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	-
GCA_018265835.1	s__CAG-103 sp018265835	81.1949	300	511	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:26:58,338] [INFO] GTDB search result was written to GCA_014869835.1_ASM1486983v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:26:58,339] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:26:58,342] [INFO] DFAST_QC result json was written to GCA_014869835.1_ASM1486983v1_genomic.fna/dqc_result.json
[2023-06-19 03:26:58,343] [INFO] DFAST_QC completed!
[2023-06-19 03:26:58,343] [INFO] Total running time: 0h0m52s