[2024-01-24 13:10:02,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:02,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:02,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference
[2024-01-24 13:10:03,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:03,931] [INFO] Task started: Prodigal
[2024-01-24 13:10:03,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg13c4a198-0ab4-487e-8341-1788eedee3ae/GCF_010448835.1_ASM1044883v1_genomic.fna.gz | prodigal -d GCF_010448835.1_ASM1044883v1_genomic.fna/cds.fna -a GCF_010448835.1_ASM1044883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:25,820] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:25,820] [INFO] Task started: HMMsearch
[2024-01-24 13:10:25,821] [INFO] Running command: hmmsearch --tblout GCF_010448835.1_ASM1044883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference/reference_markers.hmm GCF_010448835.1_ASM1044883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:26,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:26,176] [INFO] Found 6/6 markers.
[2024-01-24 13:10:26,220] [INFO] Query marker FASTA was written to GCF_010448835.1_ASM1044883v1_genomic.fna/markers.fasta
[2024-01-24 13:10:26,221] [INFO] Task started: Blastn
[2024-01-24 13:10:26,221] [INFO] Running command: blastn -query GCF_010448835.1_ASM1044883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference/reference_markers.fasta -out GCF_010448835.1_ASM1044883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:26,867] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:26,871] [INFO] Selected 6 target genomes.
[2024-01-24 13:10:26,872] [INFO] Target genome list was writen to GCF_010448835.1_ASM1044883v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:26,875] [INFO] Task started: fastANI
[2024-01-24 13:10:26,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c4a198-0ab4-487e-8341-1788eedee3ae/GCF_010448835.1_ASM1044883v1_genomic.fna.gz --refList GCF_010448835.1_ASM1044883v1_genomic.fna/target_genomes.txt --output GCF_010448835.1_ASM1044883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:34,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:34,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:34,090] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:34,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:34,091] [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 halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	100.0	1629	1631	95	conclusive
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	84.3212	1167	1631	95	below_threshold
Draconibacterium mangrovi	strain=GM2-18	GCA_010586825.1	2697469	2697469	type	True	84.076	1183	1631	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	83.7095	1116	1631	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	83.6512	1096	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:34,092] [INFO] DFAST Taxonomy check result was written to GCF_010448835.1_ASM1044883v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:34,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:34,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:34,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference/checkm_data
[2024-01-24 13:10:34,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:34,141] [INFO] Task started: CheckM
[2024-01-24 13:10:34,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010448835.1_ASM1044883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010448835.1_ASM1044883v1_genomic.fna/checkm_input GCF_010448835.1_ASM1044883v1_genomic.fna/checkm_result
[2024-01-24 13:11:36,413] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:36,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:36,436] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:36,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:36,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010448835.1_ASM1044883v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:36,437] [INFO] Task started: Blastn
[2024-01-24 13:11:36,438] [INFO] Running command: blastn -query GCF_010448835.1_ASM1044883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd1a24d-1581-4839-943d-696b0a332fd5/dqc_reference/reference_markers_gtdb.fasta -out GCF_010448835.1_ASM1044883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:37,241] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:37,245] [INFO] Selected 7 target genomes.
[2024-01-24 13:11:37,245] [INFO] Target genome list was writen to GCF_010448835.1_ASM1044883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:37,251] [INFO] Task started: fastANI
[2024-01-24 13:11:37,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c4a198-0ab4-487e-8341-1788eedee3ae/GCF_010448835.1_ASM1044883v1_genomic.fna.gz --refList GCF_010448835.1_ASM1044883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010448835.1_ASM1044883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:45,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:45,733] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:45,733] [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_010448835.1	s__Draconibacterium halophilum	100.0	1630	1631	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_000949475.1	s__Draconibacterium sediminis	84.3399	1165	1631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010586825.1	s__Draconibacterium mangrovi	84.0839	1182	1631	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	83.6906	1116	1631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_011799805.1	s__Draconibacterium sp011799805	78.453	447	1631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCA_011620585.1	s__Draconibacterium sp011620585	77.4057	279	1631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576475.1	s__Draconibacterium luteum	77.3928	343	1631	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 13:11:45,735] [INFO] GTDB search result was written to GCF_010448835.1_ASM1044883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:45,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:45,738] [INFO] DFAST_QC result json was written to GCF_010448835.1_ASM1044883v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:45,738] [INFO] DFAST_QC completed!
[2024-01-24 13:11:45,738] [INFO] Total running time: 0h1m43s