[2023-06-13 00:45:15,794] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:15,796] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:15,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference
[2023-06-13 00:45:18,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:18,180] [INFO] Task started: Prodigal
[2023-06-13 00:45:18,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg82af6e91-2cef-4607-950a-5dd93bf6c950/GCA_947459295.1_RE-18aug17-282_genomic.fna.gz | prodigal -d GCA_947459295.1_RE-18aug17-282_genomic.fna/cds.fna -a GCA_947459295.1_RE-18aug17-282_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:26,774] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:26,774] [INFO] Task started: HMMsearch
[2023-06-13 00:45:26,774] [INFO] Running command: hmmsearch --tblout GCA_947459295.1_RE-18aug17-282_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference/reference_markers.hmm GCA_947459295.1_RE-18aug17-282_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:27,039] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:27,041] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg82af6e91-2cef-4607-950a-5dd93bf6c950/GCA_947459295.1_RE-18aug17-282_genomic.fna.gz]
[2023-06-13 00:45:27,086] [INFO] Query marker FASTA was written to GCA_947459295.1_RE-18aug17-282_genomic.fna/markers.fasta
[2023-06-13 00:45:27,087] [INFO] Task started: Blastn
[2023-06-13 00:45:27,087] [INFO] Running command: blastn -query GCA_947459295.1_RE-18aug17-282_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference/reference_markers.fasta -out GCA_947459295.1_RE-18aug17-282_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:27,702] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:27,706] [INFO] Selected 28 target genomes.
[2023-06-13 00:45:27,706] [INFO] Target genome list was writen to GCA_947459295.1_RE-18aug17-282_genomic.fna/target_genomes.txt
[2023-06-13 00:45:27,716] [INFO] Task started: fastANI
[2023-06-13 00:45:27,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg82af6e91-2cef-4607-950a-5dd93bf6c950/GCA_947459295.1_RE-18aug17-282_genomic.fna.gz --refList GCA_947459295.1_RE-18aug17-282_genomic.fna/target_genomes.txt --output GCA_947459295.1_RE-18aug17-282_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:44,931] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:44,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:44,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:44,940] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:45:44,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:45:44,940] [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 goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.2973	93	721	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.1435	77	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:45:44,942] [INFO] DFAST Taxonomy check result was written to GCA_947459295.1_RE-18aug17-282_genomic.fna/tc_result.tsv
[2023-06-13 00:45:44,943] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:44,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:44,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference/checkm_data
[2023-06-13 00:45:44,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:44,975] [INFO] Task started: CheckM
[2023-06-13 00:45:44,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947459295.1_RE-18aug17-282_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947459295.1_RE-18aug17-282_genomic.fna/checkm_input GCA_947459295.1_RE-18aug17-282_genomic.fna/checkm_result
[2023-06-13 00:46:14,725] [INFO] Task succeeded: CheckM
[2023-06-13 00:46:14,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:46:14,746] [INFO] ===== Completeness check finished =====
[2023-06-13 00:46:14,747] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:46:14,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947459295.1_RE-18aug17-282_genomic.fna/markers.fasta)
[2023-06-13 00:46:14,748] [INFO] Task started: Blastn
[2023-06-13 00:46:14,748] [INFO] Running command: blastn -query GCA_947459295.1_RE-18aug17-282_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bba29d9-5ed0-4b64-b12c-463cf1ea6111/dqc_reference/reference_markers_gtdb.fasta -out GCA_947459295.1_RE-18aug17-282_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:46:15,782] [INFO] Task succeeded: Blastn
[2023-06-13 00:46:15,787] [INFO] Selected 16 target genomes.
[2023-06-13 00:46:15,787] [INFO] Target genome list was writen to GCA_947459295.1_RE-18aug17-282_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:46:15,797] [INFO] Task started: fastANI
[2023-06-13 00:46:15,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg82af6e91-2cef-4607-950a-5dd93bf6c950/GCA_947459295.1_RE-18aug17-282_genomic.fna.gz --refList GCA_947459295.1_RE-18aug17-282_genomic.fna/target_genomes_gtdb.txt --output GCA_947459295.1_RE-18aug17-282_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:46:23,713] [INFO] Task succeeded: fastANI
[2023-06-13 00:46:23,727] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 00:46:23,728] [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_903958045.1	s__Sediminibacterium sp903958045	90.57	541	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.78	99.78	0.90	0.90	2	-
GCA_017987615.1	s__Sediminibacterium sp017987615	90.2435	326	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971025.1	s__Sediminibacterium sp018971025	86.4324	464	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299885.1	s__Sediminibacterium sp002299885	77.0367	83	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983845.1	s__Sediminibacterium sp017983845	76.9087	81	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.69	99.69	0.96	0.96	2	-
GCA_017856545.1	s__Sediminibacterium sp017856545	76.8816	95	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831935.1	s__Sediminibacterium sp903831935	76.7025	151	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.28	98.68	0.92	0.87	6	-
GCA_903825095.1	s__Sediminibacterium sp903825095	76.6219	67	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.41	98.41	0.71	0.71	2	-
GCA_009924165.1	s__Sediminibacterium sp009924165	76.3115	72	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.2973	93	721	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	76.2047	104	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297995.1	s__Sediminibacterium sp013297995	76.1061	102	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256435.1	s__Sediminibacterium sp002256435	76.0209	101	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847655.1	s__Sediminibacterium sp903847655	76.0197	66	721	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:46:23,730] [INFO] GTDB search result was written to GCA_947459295.1_RE-18aug17-282_genomic.fna/result_gtdb.tsv
[2023-06-13 00:46:23,730] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:46:23,734] [INFO] DFAST_QC result json was written to GCA_947459295.1_RE-18aug17-282_genomic.fna/dqc_result.json
[2023-06-13 00:46:23,734] [INFO] DFAST_QC completed!
[2023-06-13 00:46:23,734] [INFO] Total running time: 0h1m8s