[2024-01-24 12:22:48,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference
[2024-01-24 12:22:49,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,666] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg04fc3777-b3e0-49f1-91fc-f6b5f42a2046/GCF_024220585.1_ASM2422058v1_genomic.fna.gz | prodigal -d GCF_024220585.1_ASM2422058v1_genomic.fna/cds.fna -a GCF_024220585.1_ASM2422058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:23,821] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:23,822] [INFO] Task started: HMMsearch
[2024-01-24 12:23:23,822] [INFO] Running command: hmmsearch --tblout GCF_024220585.1_ASM2422058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference/reference_markers.hmm GCF_024220585.1_ASM2422058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:24,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:24,143] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg04fc3777-b3e0-49f1-91fc-f6b5f42a2046/GCF_024220585.1_ASM2422058v1_genomic.fna.gz]
[2024-01-24 12:23:24,200] [INFO] Query marker FASTA was written to GCF_024220585.1_ASM2422058v1_genomic.fna/markers.fasta
[2024-01-24 12:23:24,201] [INFO] Task started: Blastn
[2024-01-24 12:23:24,201] [INFO] Running command: blastn -query GCF_024220585.1_ASM2422058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference/reference_markers.fasta -out GCF_024220585.1_ASM2422058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,802] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,806] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:24,807] [INFO] Target genome list was writen to GCF_024220585.1_ASM2422058v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:24,813] [INFO] Task started: fastANI
[2024-01-24 12:23:24,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg04fc3777-b3e0-49f1-91fc-f6b5f42a2046/GCF_024220585.1_ASM2422058v1_genomic.fna.gz --refList GCF_024220585.1_ASM2422058v1_genomic.fna/target_genomes.txt --output GCF_024220585.1_ASM2422058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:41,324] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:41,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:41,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:41,337] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:41,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:41,337] [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
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	80.9798	992	2408	95	below_threshold
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	80.5315	933	2408	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	80.4493	909	2408	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	77.7156	428	2408	95	below_threshold
Dyadobacter luteus	strain=RS19	GCA_003383615.1	2259619	2259619	type	True	77.5547	333	2408	95	below_threshold
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	77.4046	327	2408	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	77.3093	327	2408	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	77.1887	351	2408	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	77.0658	268	2408	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	76.9807	348	2408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:41,340] [INFO] DFAST Taxonomy check result was written to GCF_024220585.1_ASM2422058v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:41,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:41,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:41,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference/checkm_data
[2024-01-24 12:23:41,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:41,416] [INFO] Task started: CheckM
[2024-01-24 12:23:41,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024220585.1_ASM2422058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024220585.1_ASM2422058v1_genomic.fna/checkm_input GCF_024220585.1_ASM2422058v1_genomic.fna/checkm_result
[2024-01-24 12:25:11,677] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:11,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:11,701] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:11,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:11,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024220585.1_ASM2422058v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:11,702] [INFO] Task started: Blastn
[2024-01-24 12:25:11,702] [INFO] Running command: blastn -query GCF_024220585.1_ASM2422058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e47c3aa-e3ae-47ee-8008-fb32e349d353/dqc_reference/reference_markers_gtdb.fasta -out GCF_024220585.1_ASM2422058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:12,414] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:12,419] [INFO] Selected 13 target genomes.
[2024-01-24 12:25:12,419] [INFO] Target genome list was writen to GCF_024220585.1_ASM2422058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:12,964] [INFO] Task started: fastANI
[2024-01-24 12:25:12,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg04fc3777-b3e0-49f1-91fc-f6b5f42a2046/GCF_024220585.1_ASM2422058v1_genomic.fna.gz --refList GCF_024220585.1_ASM2422058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024220585.1_ASM2422058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:27,715] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:27,735] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:25:27,736] [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_900108855.1	s__Dyadobacter koreensis	80.9798	992	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	80.5311	933	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221875.1	s__Dyadobacter sp015221875	80.4422	910	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	80.127	848	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349265.1	s__Dyadobacter psychrotolerans	77.7283	426	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003383615.1	s__Dyadobacter luteus	77.5547	333	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	77.3093	327	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869225.1	s__Dyadobacter bucti	77.1887	351	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	77.0658	268	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149045.1	s__Dyadobacter flavalbus	76.9807	348	2408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:27,738] [INFO] GTDB search result was written to GCF_024220585.1_ASM2422058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:27,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:27,744] [INFO] DFAST_QC result json was written to GCF_024220585.1_ASM2422058v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:27,745] [INFO] DFAST_QC completed!
[2024-01-24 12:25:27,745] [INFO] Total running time: 0h2m39s