[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,924] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb6fcc3c-84a1-4302-a629-486e5f423623/GCF_020012125.1_ASM2001212v1_genomic.fna.gz | prodigal -d GCF_020012125.1_ASM2001212v1_genomic.fna/cds.fna -a GCF_020012125.1_ASM2001212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:40,248] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:40,249] [INFO] Task started: HMMsearch
[2024-01-24 10:47:40,249] [INFO] Running command: hmmsearch --tblout GCF_020012125.1_ASM2001212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference/reference_markers.hmm GCF_020012125.1_ASM2001212v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:40,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:40,548] [INFO] Found 6/6 markers.
[2024-01-24 10:47:40,595] [INFO] Query marker FASTA was written to GCF_020012125.1_ASM2001212v1_genomic.fna/markers.fasta
[2024-01-24 10:47:40,596] [INFO] Task started: Blastn
[2024-01-24 10:47:40,596] [INFO] Running command: blastn -query GCF_020012125.1_ASM2001212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference/reference_markers.fasta -out GCF_020012125.1_ASM2001212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:41,344] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:41,349] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:41,349] [INFO] Target genome list was writen to GCF_020012125.1_ASM2001212v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:41,444] [INFO] Task started: fastANI
[2024-01-24 10:47:41,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6fcc3c-84a1-4302-a629-486e5f423623/GCF_020012125.1_ASM2001212v1_genomic.fna.gz --refList GCF_020012125.1_ASM2001212v1_genomic.fna/target_genomes.txt --output GCF_020012125.1_ASM2001212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:59,233] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:59,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:59,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:59,247] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:59,247] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:59,248] [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 baengnokdamensis	strain=BRD72	GCA_008728635.1	2615203	2615203	type	True	82.1016	1020	1713	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	81.4775	1114	1713	95	below_threshold
Hymenobacter ginkgonis	strain=HMF4947	GCA_009755225.1	2682976	2682976	type	True	81.0572	1013	1713	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	80.8269	936	1713	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	80.0922	889	1713	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	80.0519	898	1713	95	below_threshold
Hymenobacter setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	79.8295	919	1713	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	79.3935	841	1713	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.2922	818	1713	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	79.0301	714	1713	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	78.5458	596	1713	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	78.3564	596	1713	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.3464	531	1713	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	77.8133	531	1713	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	77.6793	475	1713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:59,249] [INFO] DFAST Taxonomy check result was written to GCF_020012125.1_ASM2001212v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:59,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:59,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:59,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference/checkm_data
[2024-01-24 10:47:59,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:59,307] [INFO] Task started: CheckM
[2024-01-24 10:47:59,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020012125.1_ASM2001212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020012125.1_ASM2001212v1_genomic.fna/checkm_input GCF_020012125.1_ASM2001212v1_genomic.fna/checkm_result
[2024-01-24 10:49:11,764] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:11,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:11,795] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:11,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:11,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020012125.1_ASM2001212v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:11,797] [INFO] Task started: Blastn
[2024-01-24 10:49:11,797] [INFO] Running command: blastn -query GCF_020012125.1_ASM2001212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd286e5d1-2bb3-4cc7-b0ae-e31272081fbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_020012125.1_ASM2001212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:12,710] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:12,714] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:12,715] [INFO] Target genome list was writen to GCF_020012125.1_ASM2001212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:12,749] [INFO] Task started: fastANI
[2024-01-24 10:49:12,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6fcc3c-84a1-4302-a629-486e5f423623/GCF_020012125.1_ASM2001212v1_genomic.fna.gz --refList GCF_020012125.1_ASM2001212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020012125.1_ASM2001212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:31,811] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:31,826] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:31,827] [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_001596155.1	s__Hymenobacter sp001596155	86.1512	1277	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684095.1	s__Hymenobacter sp004684095	84.8548	1245	1713	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	82.9755	1108	1713	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	82.1199	1076	1713	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	82.1016	1020	1713	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	81.8491	1007	1713	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	81.4973	1110	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755225.1	s__Hymenobacter sp009755225	81.061	1013	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	80.8144	939	1713	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	80.2302	942	1713	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	79.8141	920	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	79.1575	671	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	78.3994	612	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	78.0885	569	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	77.9258	462	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333525.1	s__Hymenobacter sp014333525	77.88	494	1713	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 10:49:31,829] [INFO] GTDB search result was written to GCF_020012125.1_ASM2001212v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:31,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:31,833] [INFO] DFAST_QC result json was written to GCF_020012125.1_ASM2001212v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:31,833] [INFO] DFAST_QC completed!
[2024-01-24 10:49:31,833] [INFO] Total running time: 0h2m25s