[2024-01-24 15:26:55,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference
[2024-01-24 15:26:56,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,615] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,615] [INFO] Running command: gunzip -c /var/lib/cwl/stgad45b803-52e2-44d9-b4e1-67280dfdabb2/GCF_009755225.1_ASM975522v1_genomic.fna.gz | prodigal -d GCF_009755225.1_ASM975522v1_genomic.fna/cds.fna -a GCF_009755225.1_ASM975522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:30,523] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:30,523] [INFO] Task started: HMMsearch
[2024-01-24 15:27:30,523] [INFO] Running command: hmmsearch --tblout GCF_009755225.1_ASM975522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference/reference_markers.hmm GCF_009755225.1_ASM975522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:30,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:30,812] [INFO] Found 6/6 markers.
[2024-01-24 15:27:30,857] [INFO] Query marker FASTA was written to GCF_009755225.1_ASM975522v1_genomic.fna/markers.fasta
[2024-01-24 15:27:30,857] [INFO] Task started: Blastn
[2024-01-24 15:27:30,857] [INFO] Running command: blastn -query GCF_009755225.1_ASM975522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference/reference_markers.fasta -out GCF_009755225.1_ASM975522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:31,479] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:31,482] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:31,483] [INFO] Target genome list was writen to GCF_009755225.1_ASM975522v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:31,491] [INFO] Task started: fastANI
[2024-01-24 15:27:31,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgad45b803-52e2-44d9-b4e1-67280dfdabb2/GCF_009755225.1_ASM975522v1_genomic.fna.gz --refList GCF_009755225.1_ASM975522v1_genomic.fna/target_genomes.txt --output GCF_009755225.1_ASM975522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:47,995] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:47,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:47,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:48,009] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:48,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:48,010] [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
Hymenobacter ginkgonis	strain=HMF4947	GCA_009755225.1	2682976	2682976	type	True	100.0	1878	1878	95	conclusive
Hymenobacter baengnokdamensis	strain=BRD72	GCA_008728635.1	2615203	2615203	type	True	81.4784	968	1878	95	below_threshold
Hymenobacter setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	81.0313	1042	1878	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	80.4805	1061	1878	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	79.6109	804	1878	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	79.2493	772	1878	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.1774	825	1878	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	78.8474	728	1878	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	78.7793	593	1878	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	78.6092	638	1878	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.0401	526	1878	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	77.817	495	1878	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	77.8092	488	1878	95	below_threshold
Hymenobacter terrestris	strain=P5252	GCA_013377905.1	2748310	2748310	type	True	77.644	460	1878	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	77.5851	466	1878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:48,012] [INFO] DFAST Taxonomy check result was written to GCF_009755225.1_ASM975522v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:48,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:48,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:48,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference/checkm_data
[2024-01-24 15:27:48,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:48,070] [INFO] Task started: CheckM
[2024-01-24 15:27:48,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009755225.1_ASM975522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009755225.1_ASM975522v1_genomic.fna/checkm_input GCF_009755225.1_ASM975522v1_genomic.fna/checkm_result
[2024-01-24 15:29:07,569] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:07,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:07,589] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:07,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:07,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009755225.1_ASM975522v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:07,590] [INFO] Task started: Blastn
[2024-01-24 15:29:07,590] [INFO] Running command: blastn -query GCF_009755225.1_ASM975522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1237b799-ea27-43a8-840c-2918a22f2a4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009755225.1_ASM975522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:08,441] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:08,444] [INFO] Selected 11 target genomes.
[2024-01-24 15:29:08,444] [INFO] Target genome list was writen to GCF_009755225.1_ASM975522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:08,451] [INFO] Task started: fastANI
[2024-01-24 15:29:08,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgad45b803-52e2-44d9-b4e1-67280dfdabb2/GCF_009755225.1_ASM975522v1_genomic.fna.gz --refList GCF_009755225.1_ASM975522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009755225.1_ASM975522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:21,334] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:21,343] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:21,344] [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_009755225.1	s__Hymenobacter sp009755225	100.0	1878	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004684095.1	s__Hymenobacter sp004684095	82.3714	1185	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013256625.1	s__Hymenobacter sp013256625	82.0709	1071	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001596155.1	s__Hymenobacter sp001596155	81.8996	1089	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571525.1	s__Hymenobacter sp017571525	81.6924	1102	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728635.1	s__Hymenobacter baengnokdamensis	81.4626	972	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013256425.1	s__Hymenobacter sp013256425	81.2919	987	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007713685.1	s__Hymenobacter sp007713685	81.0045	1046	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427535.1	s__Hymenobacter sp016427535	80.859	1085	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927305.1	s__Hymenobacter polaris	80.4782	1062	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816125.1	s__Hymenobacter coccineus	79.7886	834	1878	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:21,345] [INFO] GTDB search result was written to GCF_009755225.1_ASM975522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:21,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:21,349] [INFO] DFAST_QC result json was written to GCF_009755225.1_ASM975522v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:21,349] [INFO] DFAST_QC completed!
[2024-01-24 15:29:21,349] [INFO] Total running time: 0h2m26s