[2024-01-24 13:17:27,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,081] [INFO] DQC Reference Directory: /var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference
[2024-01-24 13:17:28,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,263] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,264] [INFO] Running command: gunzip -c /var/lib/cwl/stg58979c4f-92d1-48dd-8313-319cb19f1979/GCF_001431365.1_ASM143136v1_genomic.fna.gz | prodigal -d GCF_001431365.1_ASM143136v1_genomic.fna/cds.fna -a GCF_001431365.1_ASM143136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:40,491] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:40,491] [INFO] Task started: HMMsearch
[2024-01-24 13:17:40,492] [INFO] Running command: hmmsearch --tblout GCF_001431365.1_ASM143136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference/reference_markers.hmm GCF_001431365.1_ASM143136v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:40,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:40,753] [INFO] Found 6/6 markers.
[2024-01-24 13:17:40,783] [INFO] Query marker FASTA was written to GCF_001431365.1_ASM143136v1_genomic.fna/markers.fasta
[2024-01-24 13:17:40,783] [INFO] Task started: Blastn
[2024-01-24 13:17:40,784] [INFO] Running command: blastn -query GCF_001431365.1_ASM143136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference/reference_markers.fasta -out GCF_001431365.1_ASM143136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:41,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:41,437] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:41,437] [INFO] Target genome list was writen to GCF_001431365.1_ASM143136v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:41,443] [INFO] Task started: fastANI
[2024-01-24 13:17:41,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg58979c4f-92d1-48dd-8313-319cb19f1979/GCF_001431365.1_ASM143136v1_genomic.fna.gz --refList GCF_001431365.1_ASM143136v1_genomic.fna/target_genomes.txt --output GCF_001431365.1_ASM143136v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:49,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:49,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:49,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:49,837] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:17:49,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:49,837] [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
Salegentibacter mishustinae	strain=KCTC 12263	GCA_001431365.1	270918	270918	type	True	100.0	1239	1240	95	conclusive
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	99.9992	1238	1240	95	conclusive
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	99.9989	1237	1240	95	conclusive
Salegentibacter mishustinae	strain=DSM 23404	GCA_003254095.1	270918	270918	type	True	99.9936	1237	1240	95	conclusive
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	92.3997	960	1240	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	84.3583	867	1240	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	83.2492	828	1240	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3786	67	1240	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.2494	94	1240	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2116	91	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:49,839] [INFO] DFAST Taxonomy check result was written to GCF_001431365.1_ASM143136v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:49,839] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:49,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:49,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference/checkm_data
[2024-01-24 13:17:49,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:49,876] [INFO] Task started: CheckM
[2024-01-24 13:17:49,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001431365.1_ASM143136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001431365.1_ASM143136v1_genomic.fna/checkm_input GCF_001431365.1_ASM143136v1_genomic.fna/checkm_result
[2024-01-24 13:18:29,017] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:29,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:29,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:29,031] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:29,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001431365.1_ASM143136v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:29,031] [INFO] Task started: Blastn
[2024-01-24 13:18:29,032] [INFO] Running command: blastn -query GCF_001431365.1_ASM143136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae5615f-90c5-4d9b-b1f4-56293f18bd43/dqc_reference/reference_markers_gtdb.fasta -out GCF_001431365.1_ASM143136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:29,981] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:29,984] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:29,984] [INFO] Target genome list was writen to GCF_001431365.1_ASM143136v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:29,997] [INFO] Task started: fastANI
[2024-01-24 13:18:29,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg58979c4f-92d1-48dd-8313-319cb19f1979/GCF_001431365.1_ASM143136v1_genomic.fna.gz --refList GCF_001431365.1_ASM143136v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001431365.1_ASM143136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:36,554] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:36,563] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:36,563] [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_002900095.1	s__Salegentibacter mishustinae	99.9992	1238	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_900168265.1	s__Salegentibacter salarius	92.4447	956	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900168045.1	s__Salegentibacter holothuriorum	86.9721	917	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	85.8014	885	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_000745315.1	s__Salegentibacter sp000745315	85.6778	921	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	85.0717	902	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168115.1	s__Salegentibacter salinarum	83.2219	846	1240	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:36,565] [INFO] GTDB search result was written to GCF_001431365.1_ASM143136v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:36,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:36,569] [INFO] DFAST_QC result json was written to GCF_001431365.1_ASM143136v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:36,569] [INFO] DFAST_QC completed!
[2024-01-24 13:18:36,569] [INFO] Total running time: 0h1m9s