[2024-01-24 12:47:24,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:24,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:24,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference
[2024-01-24 12:47:25,299] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:25,300] [INFO] Task started: Prodigal
[2024-01-24 12:47:25,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg735f683e-ba1c-4417-ab93-ee565c7a58d3/GCF_003721595.1_ASM372159v1_genomic.fna.gz | prodigal -d GCF_003721595.1_ASM372159v1_genomic.fna/cds.fna -a GCF_003721595.1_ASM372159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:47,650] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:47,650] [INFO] Task started: HMMsearch
[2024-01-24 12:47:47,650] [INFO] Running command: hmmsearch --tblout GCF_003721595.1_ASM372159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference/reference_markers.hmm GCF_003721595.1_ASM372159v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:47,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:47,997] [INFO] Found 6/6 markers.
[2024-01-24 12:47:48,037] [INFO] Query marker FASTA was written to GCF_003721595.1_ASM372159v1_genomic.fna/markers.fasta
[2024-01-24 12:47:48,038] [INFO] Task started: Blastn
[2024-01-24 12:47:48,038] [INFO] Running command: blastn -query GCF_003721595.1_ASM372159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference/reference_markers.fasta -out GCF_003721595.1_ASM372159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:48,705] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:48,709] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:48,710] [INFO] Target genome list was writen to GCF_003721595.1_ASM372159v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:48,719] [INFO] Task started: fastANI
[2024-01-24 12:47:48,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg735f683e-ba1c-4417-ab93-ee565c7a58d3/GCF_003721595.1_ASM372159v1_genomic.fna.gz --refList GCF_003721595.1_ASM372159v1_genomic.fna/target_genomes.txt --output GCF_003721595.1_ASM372159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:06,830] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:06,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:06,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:06,835] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:06,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:06,836] [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
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	100.0	1625	1628	95	conclusive
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	76.4241	205	1628	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	75.8628	62	1628	95	below_threshold
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	75.7026	58	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:06,841] [INFO] DFAST Taxonomy check result was written to GCF_003721595.1_ASM372159v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:06,842] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:06,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:06,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference/checkm_data
[2024-01-24 12:48:06,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:06,898] [INFO] Task started: CheckM
[2024-01-24 12:48:06,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721595.1_ASM372159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721595.1_ASM372159v1_genomic.fna/checkm_input GCF_003721595.1_ASM372159v1_genomic.fna/checkm_result
[2024-01-24 12:49:07,779] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:07,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:07,803] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:07,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:07,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721595.1_ASM372159v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:07,805] [INFO] Task started: Blastn
[2024-01-24 12:49:07,805] [INFO] Running command: blastn -query GCF_003721595.1_ASM372159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd09fbdc6-e5f4-43e6-b612-d2444416b60f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721595.1_ASM372159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:08,804] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:08,809] [INFO] Selected 25 target genomes.
[2024-01-24 12:49:08,809] [INFO] Target genome list was writen to GCF_003721595.1_ASM372159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:08,840] [INFO] Task started: fastANI
[2024-01-24 12:49:08,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg735f683e-ba1c-4417-ab93-ee565c7a58d3/GCF_003721595.1_ASM372159v1_genomic.fna.gz --refList GCF_003721595.1_ASM372159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721595.1_ASM372159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:24,506] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:24,531] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:24,531] [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_003721595.1	s__Ginsengibacter sp003721595	100.0	1625	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017307735.1	s__Ginsengibacter sp017307735	76.596	87	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710285.1	s__Ginsengibacter hankyongi	76.4241	205	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268075.1	s__Ginsengibacter sp018268075	76.148	118	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882215.1	s__Ginsengibacter sp017882215	75.8767	103	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898465.1	s__Ferruginibacter sp001898465	75.8758	51	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.99	99.99	0.99	0.97	3	-
GCA_016715365.1	s__Ferruginibacter sp016715365	75.8483	66	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.79	98.54	0.91	0.89	5	-
GCA_003132765.1	s__Ginsengibacter sp003132765	75.7639	75	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720775.1	s__Ferruginibacter sp016720775	75.7576	54	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288945.1	s__Puia sp013288945	75.7164	60	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374045.1	s__Segetibacter koreensis	75.6766	57	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694745.1	s__Ginsengibacter sp013694745	75.5092	72	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247895.1	s__Parafilimonas sp019247895	75.4727	51	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379625.1	s__Ferruginibacter sp014379625	75.3193	66	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268135.1	s__Ferruginibacter sp018268135	75.2232	60	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.79	99.79	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:24,534] [INFO] GTDB search result was written to GCF_003721595.1_ASM372159v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:24,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:24,538] [INFO] DFAST_QC result json was written to GCF_003721595.1_ASM372159v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:24,538] [INFO] DFAST_QC completed!
[2024-01-24 12:49:24,538] [INFO] Total running time: 0h2m0s