[2023-06-28 23:30:22,195] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:30:22,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:30:22,199] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference
[2023-06-28 23:30:23,437] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:30:23,438] [INFO] Task started: Prodigal
[2023-06-28 23:30:23,438] [INFO] Running command: gunzip -c /var/lib/cwl/stge0a3f880-df17-4245-8d98-8ff22b9760ee/GCA_020403685.1_ASM2040368v1_genomic.fna.gz | prodigal -d GCA_020403685.1_ASM2040368v1_genomic.fna/cds.fna -a GCA_020403685.1_ASM2040368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:30:37,805] [INFO] Task succeeded: Prodigal
[2023-06-28 23:30:37,805] [INFO] Task started: HMMsearch
[2023-06-28 23:30:37,805] [INFO] Running command: hmmsearch --tblout GCA_020403685.1_ASM2040368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference/reference_markers.hmm GCA_020403685.1_ASM2040368v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:30:38,036] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:30:38,037] [INFO] Found 6/6 markers.
[2023-06-28 23:30:38,065] [INFO] Query marker FASTA was written to GCA_020403685.1_ASM2040368v1_genomic.fna/markers.fasta
[2023-06-28 23:30:38,066] [INFO] Task started: Blastn
[2023-06-28 23:30:38,066] [INFO] Running command: blastn -query GCA_020403685.1_ASM2040368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference/reference_markers.fasta -out GCA_020403685.1_ASM2040368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:30:38,651] [INFO] Task succeeded: Blastn
[2023-06-28 23:30:38,656] [INFO] Selected 20 target genomes.
[2023-06-28 23:30:38,656] [INFO] Target genome list was writen to GCA_020403685.1_ASM2040368v1_genomic.fna/target_genomes.txt
[2023-06-28 23:30:38,659] [INFO] Task started: fastANI
[2023-06-28 23:30:38,659] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a3f880-df17-4245-8d98-8ff22b9760ee/GCA_020403685.1_ASM2040368v1_genomic.fna.gz --refList GCA_020403685.1_ASM2040368v1_genomic.fna/target_genomes.txt --output GCA_020403685.1_ASM2040368v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:30:51,960] [INFO] Task succeeded: fastANI
[2023-06-28 23:30:51,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:30:51,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:30:51,974] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:30:51,974] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:30:51,975] [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
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	76.6034	61	879	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.5481	54	879	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	76.4866	50	879	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.2402	71	879	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	75.9489	66	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:30:51,977] [INFO] DFAST Taxonomy check result was written to GCA_020403685.1_ASM2040368v1_genomic.fna/tc_result.tsv
[2023-06-28 23:30:51,977] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:30:51,977] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:30:51,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference/checkm_data
[2023-06-28 23:30:51,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:30:52,014] [INFO] Task started: CheckM
[2023-06-28 23:30:52,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020403685.1_ASM2040368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020403685.1_ASM2040368v1_genomic.fna/checkm_input GCA_020403685.1_ASM2040368v1_genomic.fna/checkm_result
[2023-06-28 23:31:37,358] [INFO] Task succeeded: CheckM
[2023-06-28 23:31:37,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:31:37,380] [INFO] ===== Completeness check finished =====
[2023-06-28 23:31:37,380] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:31:37,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020403685.1_ASM2040368v1_genomic.fna/markers.fasta)
[2023-06-28 23:31:37,381] [INFO] Task started: Blastn
[2023-06-28 23:31:37,381] [INFO] Running command: blastn -query GCA_020403685.1_ASM2040368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7c446d1-f96c-4ebb-9a1c-7c19d7917672/dqc_reference/reference_markers_gtdb.fasta -out GCA_020403685.1_ASM2040368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:31:38,121] [INFO] Task succeeded: Blastn
[2023-06-28 23:31:38,125] [INFO] Selected 25 target genomes.
[2023-06-28 23:31:38,125] [INFO] Target genome list was writen to GCA_020403685.1_ASM2040368v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:31:38,128] [INFO] Task started: fastANI
[2023-06-28 23:31:38,128] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a3f880-df17-4245-8d98-8ff22b9760ee/GCA_020403685.1_ASM2040368v1_genomic.fna.gz --refList GCA_020403685.1_ASM2040368v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020403685.1_ASM2040368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:31:50,592] [INFO] Task succeeded: fastANI
[2023-06-28 23:31:50,609] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:31:50,609] [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
GCA_903899675.1	s__Sediminibacterium sp903899675	76.8614	121	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.92	99.92	0.95	0.95	2	-
GCF_900167075.1	s__Sediminibacterium ginsengisoli	76.5481	54	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183765.1	s__Sediminibacterium sp016183765	76.5197	65	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270485.1	s__Sediminibacterium sp012270485	76.3472	68	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913355.1	s__Sediminibacterium sp903913355	76.3354	69	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973575.1	s__Sediminibacterium magnilacihabitans	76.3271	62	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.08	98.17	0.92	0.85	3	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.2188	72	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013391385.1	s__Sediminibacterium sp013391385	76.1489	63	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511175.1	s__Sediminibacterium salmoneum	75.971	65	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028765.1	s__Sediminibacterium sp004028765	75.8591	82	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508085.1	s__Sediminibacterium sp000508085	75.7942	63	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903926855.1	s__Sediminibacterium sp903926855	75.7723	72	879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.86	97.42	0.87	0.81	7	-
--------------------------------------------------------------------------------
[2023-06-28 23:31:50,613] [INFO] GTDB search result was written to GCA_020403685.1_ASM2040368v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:31:50,613] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:31:50,616] [INFO] DFAST_QC result json was written to GCA_020403685.1_ASM2040368v1_genomic.fna/dqc_result.json
[2023-06-28 23:31:50,616] [INFO] DFAST_QC completed!
[2023-06-28 23:31:50,617] [INFO] Total running time: 0h1m28s