[2024-01-25 19:05:05,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:05,530] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:05,530] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference
[2024-01-25 19:05:06,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:06,702] [INFO] Task started: Prodigal
[2024-01-25 19:05:06,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f7f1667-a15e-4a8b-b3a2-2f715aadd83f/GCF_030056665.1_ASM3005666v1_genomic.fna.gz | prodigal -d GCF_030056665.1_ASM3005666v1_genomic.fna/cds.fna -a GCF_030056665.1_ASM3005666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:29,734] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:29,734] [INFO] Task started: HMMsearch
[2024-01-25 19:05:29,734] [INFO] Running command: hmmsearch --tblout GCF_030056665.1_ASM3005666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference/reference_markers.hmm GCF_030056665.1_ASM3005666v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:30,035] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:30,036] [INFO] Found 6/6 markers.
[2024-01-25 19:05:30,085] [INFO] Query marker FASTA was written to GCF_030056665.1_ASM3005666v1_genomic.fna/markers.fasta
[2024-01-25 19:05:30,085] [INFO] Task started: Blastn
[2024-01-25 19:05:30,086] [INFO] Running command: blastn -query GCF_030056665.1_ASM3005666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference/reference_markers.fasta -out GCF_030056665.1_ASM3005666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:30,654] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:30,656] [INFO] Selected 19 target genomes.
[2024-01-25 19:05:30,656] [INFO] Target genome list was writen to GCF_030056665.1_ASM3005666v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:30,681] [INFO] Task started: fastANI
[2024-01-25 19:05:30,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7f1667-a15e-4a8b-b3a2-2f715aadd83f/GCF_030056665.1_ASM3005666v1_genomic.fna.gz --refList GCF_030056665.1_ASM3005666v1_genomic.fna/target_genomes.txt --output GCF_030056665.1_ASM3005666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:44,234] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:44,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:44,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:44,242] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:05:44,243] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:05:44,243] [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
Flectobacillus major	strain=DSM 103	GCA_000427405.1	103	103	type	True	79.2798	697	2170	95	below_threshold
Arcicella aurantiaca	strain=DSM 22214	GCA_003148625.1	591202	591202	type	True	77.0207	315	2170	95	below_threshold
Aquirufa antheringensis	strain=30S-ANTBAC	GCA_004307425.1	2516559	2516559	type	True	76.5278	57	2170	95	below_threshold
Sandaracinomonas limnophila	strain=FSY-15	GCA_004005965.1	1862386	1862386	type	True	76.5046	73	2170	95	below_threshold
Aquirufa lenticrescens	strain=9H-EGSE	GCA_019916085.1	2696560	2696560	type	True	76.4314	65	2170	95	below_threshold
Aquirufa rosea	strain=CAR-16	GCA_004118285.1	2509241	2509241	type	True	76.4089	65	2170	95	below_threshold
Aquirufa aurantiipilula	strain=15D-MOB	GCA_019923745.1	2696561	2696561	type	True	76.117	76	2170	95	below_threshold
Aquirufa nivalisilvae	strain=59G-WUEMPEL	GCA_004307455.1	2516557	2516557	type	True	75.8877	73	2170	95	below_threshold
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	75.5206	51	2170	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	75.5027	60	2170	95	below_threshold
Flammeovirga aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	75.4255	67	2170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:44,244] [INFO] DFAST Taxonomy check result was written to GCF_030056665.1_ASM3005666v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:44,245] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:44,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:44,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference/checkm_data
[2024-01-25 19:05:44,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:44,309] [INFO] Task started: CheckM
[2024-01-25 19:05:44,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030056665.1_ASM3005666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030056665.1_ASM3005666v1_genomic.fna/checkm_input GCF_030056665.1_ASM3005666v1_genomic.fna/checkm_result
[2024-01-25 19:06:48,584] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:48,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:48,614] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:48,615] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:48,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030056665.1_ASM3005666v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:48,616] [INFO] Task started: Blastn
[2024-01-25 19:06:48,616] [INFO] Running command: blastn -query GCF_030056665.1_ASM3005666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e1ba5b-4ce4-4804-afcd-105b1fc4c0d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_030056665.1_ASM3005666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:49,410] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:49,413] [INFO] Selected 12 target genomes.
[2024-01-25 19:06:49,413] [INFO] Target genome list was writen to GCF_030056665.1_ASM3005666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:49,423] [INFO] Task started: fastANI
[2024-01-25 19:06:49,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7f1667-a15e-4a8b-b3a2-2f715aadd83f/GCF_030056665.1_ASM3005666v1_genomic.fna.gz --refList GCF_030056665.1_ASM3005666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030056665.1_ASM3005666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:04,493] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:04,501] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:04,501] [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_002270355.1	s__Flectobacillus sp002270355	97.0108	1882	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	97.63	97.63	0.89	0.89	2	conclusive
GCF_009905545.1	s__Flectobacillus sp009905545	90.6704	1802	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427405.1	s__Flectobacillus major	79.3105	697	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298025.1	s__Flectobacillus sp013298025	78.1848	458	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204325.1	s__Arcicella rosea	77.1507	340	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148625.1	s__Arcicella aurantiaca	77.0285	314	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115665.1	s__Pseudarcicella hirudinis	76.9856	164	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Pseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298125.1	s__Arcicella sp013298125	76.2963	187	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298865.1	s__JAAFJL01 sp013298865	76.1885	148	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__JAAFJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108855.1	s__Dyadobacter koreensis	75.5206	51	2170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:04,503] [INFO] GTDB search result was written to GCF_030056665.1_ASM3005666v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:04,504] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:04,506] [INFO] DFAST_QC result json was written to GCF_030056665.1_ASM3005666v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:04,506] [INFO] DFAST_QC completed!
[2024-01-25 19:07:04,506] [INFO] Total running time: 0h1m59s