[2024-01-24 13:36:45,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference
[2024-01-24 13:36:46,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,339] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg662d8273-99b5-4f95-8b18-a732c23aeeb2/GCF_014397245.1_ASM1439724v1_genomic.fna.gz | prodigal -d GCF_014397245.1_ASM1439724v1_genomic.fna/cds.fna -a GCF_014397245.1_ASM1439724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:09,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:09,774] [INFO] Task started: HMMsearch
[2024-01-24 13:37:09,774] [INFO] Running command: hmmsearch --tblout GCF_014397245.1_ASM1439724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference/reference_markers.hmm GCF_014397245.1_ASM1439724v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:10,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:10,046] [INFO] Found 6/6 markers.
[2024-01-24 13:37:10,090] [INFO] Query marker FASTA was written to GCF_014397245.1_ASM1439724v1_genomic.fna/markers.fasta
[2024-01-24 13:37:10,090] [INFO] Task started: Blastn
[2024-01-24 13:37:10,090] [INFO] Running command: blastn -query GCF_014397245.1_ASM1439724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference/reference_markers.fasta -out GCF_014397245.1_ASM1439724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:10,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:10,812] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:10,813] [INFO] Target genome list was writen to GCF_014397245.1_ASM1439724v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:10,820] [INFO] Task started: fastANI
[2024-01-24 13:37:10,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg662d8273-99b5-4f95-8b18-a732c23aeeb2/GCF_014397245.1_ASM1439724v1_genomic.fna.gz --refList GCF_014397245.1_ASM1439724v1_genomic.fna/target_genomes.txt --output GCF_014397245.1_ASM1439724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:21,836] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:21,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:21,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:21,845] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:21,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:21,845] [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
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	100.0	1764	1767	95	conclusive
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	88.8886	1361	1767	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	85.8848	1284	1767	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	83.4748	1182	1767	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	82.5148	1205	1767	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.6065	112	1767	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.471	64	1767	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.0877	64	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:21,847] [INFO] DFAST Taxonomy check result was written to GCF_014397245.1_ASM1439724v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:21,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:21,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:21,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference/checkm_data
[2024-01-24 13:37:21,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:21,900] [INFO] Task started: CheckM
[2024-01-24 13:37:21,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014397245.1_ASM1439724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014397245.1_ASM1439724v1_genomic.fna/checkm_input GCF_014397245.1_ASM1439724v1_genomic.fna/checkm_result
[2024-01-24 13:38:26,741] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:26,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:26,758] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:26,758] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:26,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014397245.1_ASM1439724v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:26,759] [INFO] Task started: Blastn
[2024-01-24 13:38:26,759] [INFO] Running command: blastn -query GCF_014397245.1_ASM1439724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96e56052-7467-4ae6-aa41-10d313dcb804/dqc_reference/reference_markers_gtdb.fasta -out GCF_014397245.1_ASM1439724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:27,607] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:27,611] [INFO] Selected 7 target genomes.
[2024-01-24 13:38:27,611] [INFO] Target genome list was writen to GCF_014397245.1_ASM1439724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:27,614] [INFO] Task started: fastANI
[2024-01-24 13:38:27,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg662d8273-99b5-4f95-8b18-a732c23aeeb2/GCF_014397245.1_ASM1439724v1_genomic.fna.gz --refList GCF_014397245.1_ASM1439724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014397245.1_ASM1439724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:36,550] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:36,557] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:36,557] [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_014397245.1	s__Arenibacter arenosicollis	100.0	1764	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002909255.1	s__Arenibacter hampyeongensis	88.8854	1361	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	85.8859	1283	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	85.1558	1277	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	83.458	1184	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	82.5129	1205	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_003201775.1	s__Arenibacter sp003201775	82.4912	1115	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:36,559] [INFO] GTDB search result was written to GCF_014397245.1_ASM1439724v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:36,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:36,562] [INFO] DFAST_QC result json was written to GCF_014397245.1_ASM1439724v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:36,562] [INFO] DFAST_QC completed!
[2024-01-24 13:38:36,562] [INFO] Total running time: 0h1m52s