[2023-06-27 11:32:57,697] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:32:57,703] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:32:57,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference
[2023-06-27 11:32:59,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:32:59,017] [INFO] Task started: Prodigal
[2023-06-27 11:32:59,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg1704a27d-540c-4920-b326-ffb9f859300d/GCA_002238445.1_ASM223844v1_genomic.fna.gz | prodigal -d GCA_002238445.1_ASM223844v1_genomic.fna/cds.fna -a GCA_002238445.1_ASM223844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:33:15,054] [INFO] Task succeeded: Prodigal
[2023-06-27 11:33:15,055] [INFO] Task started: HMMsearch
[2023-06-27 11:33:15,055] [INFO] Running command: hmmsearch --tblout GCA_002238445.1_ASM223844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference/reference_markers.hmm GCA_002238445.1_ASM223844v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:33:15,404] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:33:15,406] [INFO] Found 6/6 markers.
[2023-06-27 11:33:15,454] [INFO] Query marker FASTA was written to GCA_002238445.1_ASM223844v1_genomic.fna/markers.fasta
[2023-06-27 11:33:15,454] [INFO] Task started: Blastn
[2023-06-27 11:33:15,454] [INFO] Running command: blastn -query GCA_002238445.1_ASM223844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference/reference_markers.fasta -out GCA_002238445.1_ASM223844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:33:16,113] [INFO] Task succeeded: Blastn
[2023-06-27 11:33:16,117] [INFO] Selected 30 target genomes.
[2023-06-27 11:33:16,117] [INFO] Target genome list was writen to GCA_002238445.1_ASM223844v1_genomic.fna/target_genomes.txt
[2023-06-27 11:33:16,124] [INFO] Task started: fastANI
[2023-06-27 11:33:16,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg1704a27d-540c-4920-b326-ffb9f859300d/GCA_002238445.1_ASM223844v1_genomic.fna.gz --refList GCA_002238445.1_ASM223844v1_genomic.fna/target_genomes.txt --output GCA_002238445.1_ASM223844v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:33:37,640] [INFO] Task succeeded: fastANI
[2023-06-27 11:33:37,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:33:37,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:33:37,648] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:33:37,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:33:37,648] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.986	108	1786	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:33:37,651] [INFO] DFAST Taxonomy check result was written to GCA_002238445.1_ASM223844v1_genomic.fna/tc_result.tsv
[2023-06-27 11:33:37,651] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:33:37,651] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:33:37,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference/checkm_data
[2023-06-27 11:33:37,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:33:37,722] [INFO] Task started: CheckM
[2023-06-27 11:33:37,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002238445.1_ASM223844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002238445.1_ASM223844v1_genomic.fna/checkm_input GCA_002238445.1_ASM223844v1_genomic.fna/checkm_result
[2023-06-27 11:34:25,658] [INFO] Task succeeded: CheckM
[2023-06-27 11:34:25,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:34:25,689] [INFO] ===== Completeness check finished =====
[2023-06-27 11:34:25,690] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:34:25,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002238445.1_ASM223844v1_genomic.fna/markers.fasta)
[2023-06-27 11:34:25,691] [INFO] Task started: Blastn
[2023-06-27 11:34:25,691] [INFO] Running command: blastn -query GCA_002238445.1_ASM223844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4973fd0a-f4d9-4ffa-b18d-e03cf3ea0919/dqc_reference/reference_markers_gtdb.fasta -out GCA_002238445.1_ASM223844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:34:26,619] [INFO] Task succeeded: Blastn
[2023-06-27 11:34:26,623] [INFO] Selected 13 target genomes.
[2023-06-27 11:34:26,624] [INFO] Target genome list was writen to GCA_002238445.1_ASM223844v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:34:26,631] [INFO] Task started: fastANI
[2023-06-27 11:34:26,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg1704a27d-540c-4920-b326-ffb9f859300d/GCA_002238445.1_ASM223844v1_genomic.fna.gz --refList GCA_002238445.1_ASM223844v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002238445.1_ASM223844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:34:43,113] [INFO] Task succeeded: fastANI
[2023-06-27 11:34:43,123] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:34:43,123] [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_002238445.1	s__Bin5 sp002238445	100.0	1784	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009841235.1	s__Bin5 sp009841235	82.1205	1063	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	95.53	95.53	0.91	0.91	2	-
GCA_011523365.1	s__Bin5 sp011523365	81.9646	1092	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840225.1	s__Bin5 sp009840225	81.9567	1003	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	-
GCA_009838625.1	s__Bin5 sp009838625	81.5727	1011	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	99.90	99.90	0.97	0.97	2	-
GCF_006569185.1	s__Litorilinea aerophila	75.986	108	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_003577005.1	s__CFX5 sp003577005	75.5309	61	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__CFX5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861025.1	s__Caldilinea sp016861025	75.3257	70	1786	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:34:43,132] [INFO] GTDB search result was written to GCA_002238445.1_ASM223844v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:34:43,132] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:34:43,153] [INFO] DFAST_QC result json was written to GCA_002238445.1_ASM223844v1_genomic.fna/dqc_result.json
[2023-06-27 11:34:43,153] [INFO] DFAST_QC completed!
[2023-06-27 11:34:43,154] [INFO] Total running time: 0h1m45s