[2023-06-13 10:11:31,336] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:11:31,339] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:11:31,340] [INFO] DQC Reference Directory: /var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference
[2023-06-13 10:11:32,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:11:32,551] [INFO] Task started: Prodigal
[2023-06-13 10:11:32,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg39c9f855-230a-4ae2-a519-7c0b7cd8b3e7/GCA_022792495.1_ASM2279249v1_genomic.fna.gz | prodigal -d GCA_022792495.1_ASM2279249v1_genomic.fna/cds.fna -a GCA_022792495.1_ASM2279249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:11:38,510] [INFO] Task succeeded: Prodigal
[2023-06-13 10:11:38,510] [INFO] Task started: HMMsearch
[2023-06-13 10:11:38,511] [INFO] Running command: hmmsearch --tblout GCA_022792495.1_ASM2279249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference/reference_markers.hmm GCA_022792495.1_ASM2279249v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:11:38,747] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:11:38,748] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg39c9f855-230a-4ae2-a519-7c0b7cd8b3e7/GCA_022792495.1_ASM2279249v1_genomic.fna.gz]
[2023-06-13 10:11:38,774] [INFO] Query marker FASTA was written to GCA_022792495.1_ASM2279249v1_genomic.fna/markers.fasta
[2023-06-13 10:11:38,775] [INFO] Task started: Blastn
[2023-06-13 10:11:38,775] [INFO] Running command: blastn -query GCA_022792495.1_ASM2279249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference/reference_markers.fasta -out GCA_022792495.1_ASM2279249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:39,272] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:39,276] [INFO] Selected 12 target genomes.
[2023-06-13 10:11:39,277] [INFO] Target genome list was writen to GCA_022792495.1_ASM2279249v1_genomic.fna/target_genomes.txt
[2023-06-13 10:11:39,279] [INFO] Task started: fastANI
[2023-06-13 10:11:39,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg39c9f855-230a-4ae2-a519-7c0b7cd8b3e7/GCA_022792495.1_ASM2279249v1_genomic.fna.gz --refList GCA_022792495.1_ASM2279249v1_genomic.fna/target_genomes.txt --output GCA_022792495.1_ASM2279249v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:44,977] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:44,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:44,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:44,991] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:44,991] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:11:44,991] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.9089	131	565	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.8849	159	565	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.8218	164	565	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.4117	116	565	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.152	59	565	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.5398	56	565	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.5398	56	565	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.3721	53	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:11:44,994] [INFO] DFAST Taxonomy check result was written to GCA_022792495.1_ASM2279249v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:44,994] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:44,995] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:44,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference/checkm_data
[2023-06-13 10:11:44,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:45,032] [INFO] Task started: CheckM
[2023-06-13 10:11:45,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022792495.1_ASM2279249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022792495.1_ASM2279249v1_genomic.fna/checkm_input GCA_022792495.1_ASM2279249v1_genomic.fna/checkm_result
[2023-06-13 10:12:08,070] [INFO] Task succeeded: CheckM
[2023-06-13 10:12:08,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:12:08,092] [INFO] ===== Completeness check finished =====
[2023-06-13 10:12:08,093] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:12:08,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022792495.1_ASM2279249v1_genomic.fna/markers.fasta)
[2023-06-13 10:12:08,093] [INFO] Task started: Blastn
[2023-06-13 10:12:08,094] [INFO] Running command: blastn -query GCA_022792495.1_ASM2279249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8dfb1729-0dba-4ae1-99f0-5897312a83ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_022792495.1_ASM2279249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:12:08,591] [INFO] Task succeeded: Blastn
[2023-06-13 10:12:08,597] [INFO] Selected 11 target genomes.
[2023-06-13 10:12:08,597] [INFO] Target genome list was writen to GCA_022792495.1_ASM2279249v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:12:08,604] [INFO] Task started: fastANI
[2023-06-13 10:12:08,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg39c9f855-230a-4ae2-a519-7c0b7cd8b3e7/GCA_022792495.1_ASM2279249v1_genomic.fna.gz --refList GCA_022792495.1_ASM2279249v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022792495.1_ASM2279249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:12:13,291] [INFO] Task succeeded: fastANI
[2023-06-13 10:12:13,307] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:12:13,307] [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_900543935.1	s__Marseille-P3106 sp900543935	79.7177	233	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905219705.1	s__Marseille-P3106 sp905219705	79.386	247	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588975.1	s__Marseille-P3106 sp910588975	79.0623	192	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937415.1	s__Marseille-P3106 sp017937415	78.9348	174	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587345.1	s__Marseille-P3106 sp910587345	78.8809	181	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585735.1	s__Marseille-P3106 sp910585735	78.602	179	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577415.1	s__Marseille-P3106 sp910577415	78.5481	181	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169975.1	s__Marseille-P3106 sp900169975	78.4623	204	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159265.1	s__Flavonifractor sp002159265	77.8193	156	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161085.1	s__Flavonifractor avicola	77.6599	143	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.94	96.68	0.83	0.78	7	-
GCF_016901735.1	s__An92 sp016901735	77.6058	141	565	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.81	98.81	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-13 10:12:13,310] [INFO] GTDB search result was written to GCA_022792495.1_ASM2279249v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:12:13,310] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:12:13,316] [INFO] DFAST_QC result json was written to GCA_022792495.1_ASM2279249v1_genomic.fna/dqc_result.json
[2023-06-13 10:12:13,316] [INFO] DFAST_QC completed!
[2023-06-13 10:12:13,316] [INFO] Total running time: 0h0m42s