[2024-01-24 13:01:53,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,338] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference
[2024-01-24 13:01:54,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,642] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,642] [INFO] Running command: gunzip -c /var/lib/cwl/stga2856df2-14ad-4067-b66e-d929acfb37f0/GCF_000949475.1_ASM94947v1_genomic.fna.gz | prodigal -d GCF_000949475.1_ASM94947v1_genomic.fna/cds.fna -a GCF_000949475.1_ASM94947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:23,053] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:23,053] [INFO] Task started: HMMsearch
[2024-01-24 13:02:23,053] [INFO] Running command: hmmsearch --tblout GCF_000949475.1_ASM94947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference/reference_markers.hmm GCF_000949475.1_ASM94947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:23,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:23,471] [INFO] Found 6/6 markers.
[2024-01-24 13:02:23,520] [INFO] Query marker FASTA was written to GCF_000949475.1_ASM94947v1_genomic.fna/markers.fasta
[2024-01-24 13:02:23,521] [INFO] Task started: Blastn
[2024-01-24 13:02:23,521] [INFO] Running command: blastn -query GCF_000949475.1_ASM94947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference/reference_markers.fasta -out GCF_000949475.1_ASM94947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:24,125] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:24,129] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:24,129] [INFO] Target genome list was writen to GCF_000949475.1_ASM94947v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:24,145] [INFO] Task started: fastANI
[2024-01-24 13:02:24,145] [INFO] Running command: fastANI --query /var/lib/cwl/stga2856df2-14ad-4067-b66e-d929acfb37f0/GCF_000949475.1_ASM94947v1_genomic.fna.gz --refList GCF_000949475.1_ASM94947v1_genomic.fna/target_genomes.txt --output GCF_000949475.1_ASM94947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:34,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:34,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:34,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:34,641] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:34,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:34,642] [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
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	100.0	1990	1990	95	conclusive
Draconibacterium mangrovi	strain=GM2-18	GCA_010586825.1	2697469	2697469	type	True	93.5268	1499	1990	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	87.6354	1260	1990	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	87.6337	1268	1990	95	below_threshold
Draconibacterium halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	84.326	1174	1990	95	below_threshold
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	76.8046	265	1990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,643] [INFO] DFAST Taxonomy check result was written to GCF_000949475.1_ASM94947v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:34,644] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:34,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:34,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference/checkm_data
[2024-01-24 13:02:34,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:34,707] [INFO] Task started: CheckM
[2024-01-24 13:02:34,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000949475.1_ASM94947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000949475.1_ASM94947v1_genomic.fna/checkm_input GCF_000949475.1_ASM94947v1_genomic.fna/checkm_result
[2024-01-24 13:03:49,862] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:49,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:49,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:49,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:49,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000949475.1_ASM94947v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:49,888] [INFO] Task started: Blastn
[2024-01-24 13:03:49,888] [INFO] Running command: blastn -query GCF_000949475.1_ASM94947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8fb4633-0e4c-41c8-a598-b47e1785f88c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000949475.1_ASM94947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:50,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:50,676] [INFO] Selected 7 target genomes.
[2024-01-24 13:03:50,676] [INFO] Target genome list was writen to GCF_000949475.1_ASM94947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:50,685] [INFO] Task started: fastANI
[2024-01-24 13:03:50,685] [INFO] Running command: fastANI --query /var/lib/cwl/stga2856df2-14ad-4067-b66e-d929acfb37f0/GCF_000949475.1_ASM94947v1_genomic.fna.gz --refList GCF_000949475.1_ASM94947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000949475.1_ASM94947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:59,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:59,713] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:59,713] [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_000949475.1	s__Draconibacterium sediminis	100.0	1990	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010586825.1	s__Draconibacterium mangrovi	93.5268	1499	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626635.1	s__Draconibacterium orientale	87.6258	1269	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010448835.1	s__Draconibacterium halophilum	84.3428	1172	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011799805.1	s__Draconibacterium sp011799805	79.9712	599	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCF_003576475.1	s__Draconibacterium luteum	77.7033	417	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493625.1	s__Draconibacterium sp015493625	76.6819	136	1990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:59,714] [INFO] GTDB search result was written to GCF_000949475.1_ASM94947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:59,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:59,718] [INFO] DFAST_QC result json was written to GCF_000949475.1_ASM94947v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:59,718] [INFO] DFAST_QC completed!
[2024-01-24 13:03:59,718] [INFO] Total running time: 0h2m6s