[2023-06-13 08:42:51,768] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:42:51,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:42:51,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference
[2023-06-13 08:42:54,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:42:54,029] [INFO] Task started: Prodigal
[2023-06-13 08:42:54,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f4b42a0-73ec-4075-9bb7-4d1774fed982/GCA_947448075.1_Jr-11may16-303_genomic.fna.gz | prodigal -d GCA_947448075.1_Jr-11may16-303_genomic.fna/cds.fna -a GCA_947448075.1_Jr-11may16-303_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:43:01,173] [INFO] Task succeeded: Prodigal
[2023-06-13 08:43:01,174] [INFO] Task started: HMMsearch
[2023-06-13 08:43:01,174] [INFO] Running command: hmmsearch --tblout GCA_947448075.1_Jr-11may16-303_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference/reference_markers.hmm GCA_947448075.1_Jr-11may16-303_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:43:01,393] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:43:01,394] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8f4b42a0-73ec-4075-9bb7-4d1774fed982/GCA_947448075.1_Jr-11may16-303_genomic.fna.gz]
[2023-06-13 08:43:01,439] [INFO] Query marker FASTA was written to GCA_947448075.1_Jr-11may16-303_genomic.fna/markers.fasta
[2023-06-13 08:43:01,440] [INFO] Task started: Blastn
[2023-06-13 08:43:01,440] [INFO] Running command: blastn -query GCA_947448075.1_Jr-11may16-303_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference/reference_markers.fasta -out GCA_947448075.1_Jr-11may16-303_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:43:02,037] [INFO] Task succeeded: Blastn
[2023-06-13 08:43:02,042] [INFO] Selected 19 target genomes.
[2023-06-13 08:43:02,043] [INFO] Target genome list was writen to GCA_947448075.1_Jr-11may16-303_genomic.fna/target_genomes.txt
[2023-06-13 08:43:02,048] [INFO] Task started: fastANI
[2023-06-13 08:43:02,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4b42a0-73ec-4075-9bb7-4d1774fed982/GCA_947448075.1_Jr-11may16-303_genomic.fna.gz --refList GCA_947448075.1_Jr-11may16-303_genomic.fna/target_genomes.txt --output GCA_947448075.1_Jr-11may16-303_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:43:17,740] [INFO] Task succeeded: fastANI
[2023-06-13 08:43:17,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:43:17,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:43:17,750] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:43:17,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:43:17,751] [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 salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.7218	78	545	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.6466	77	545	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.2038	61	545	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:43:17,753] [INFO] DFAST Taxonomy check result was written to GCA_947448075.1_Jr-11may16-303_genomic.fna/tc_result.tsv
[2023-06-13 08:43:17,754] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:43:17,754] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:43:17,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference/checkm_data
[2023-06-13 08:43:17,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:43:17,783] [INFO] Task started: CheckM
[2023-06-13 08:43:17,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947448075.1_Jr-11may16-303_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947448075.1_Jr-11may16-303_genomic.fna/checkm_input GCA_947448075.1_Jr-11may16-303_genomic.fna/checkm_result
[2023-06-13 08:43:44,474] [INFO] Task succeeded: CheckM
[2023-06-13 08:43:44,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:43:44,501] [INFO] ===== Completeness check finished =====
[2023-06-13 08:43:44,501] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:43:44,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947448075.1_Jr-11may16-303_genomic.fna/markers.fasta)
[2023-06-13 08:43:44,502] [INFO] Task started: Blastn
[2023-06-13 08:43:44,502] [INFO] Running command: blastn -query GCA_947448075.1_Jr-11may16-303_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f4b9d6e-2539-449f-8bc6-4ff290dfc88a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947448075.1_Jr-11may16-303_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:43:45,342] [INFO] Task succeeded: Blastn
[2023-06-13 08:43:45,347] [INFO] Selected 13 target genomes.
[2023-06-13 08:43:45,347] [INFO] Target genome list was writen to GCA_947448075.1_Jr-11may16-303_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:43:45,357] [INFO] Task started: fastANI
[2023-06-13 08:43:45,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4b42a0-73ec-4075-9bb7-4d1774fed982/GCA_947448075.1_Jr-11may16-303_genomic.fna.gz --refList GCA_947448075.1_Jr-11may16-303_genomic.fna/target_genomes_gtdb.txt --output GCA_947448075.1_Jr-11may16-303_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:43:51,901] [INFO] Task succeeded: fastANI
[2023-06-13 08:43:51,917] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:43:51,917] [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_903831935.1	s__Sediminibacterium sp903831935	98.7241	495	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.28	98.68	0.92	0.87	6	conclusive
GCA_002256765.1	s__Sediminibacterium sp002256765	78.1012	173	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.72	99.72	0.88	0.88	2	-
GCA_002256435.1	s__Sediminibacterium sp002256435	77.879	210	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825065.1	s__Sediminibacterium sp903825065	77.87	127	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.09	98.06	0.72	0.65	3	-
GCA_903933995.1	s__Sediminibacterium sp903933995	77.8373	140	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927185.1	s__Sediminibacterium sp903927185	77.6494	172	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.80	99.71	0.93	0.90	3	-
GCA_002281575.1	s__Sediminibacterium sp002281575	77.3935	114	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821465.1	s__Sediminibacterium sp903821465	77.2795	171	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924075.1	s__Sediminibacterium sp903924075	77.2315	145	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903874055.1	s__Sediminibacterium sp903874055	77.0285	74	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.58	99.40	0.88	0.85	9	-
GCA_004294465.1	s__Sediminibacterium sp004294465	76.8632	69	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004294135.1	s__Sediminibacterium sp004294135	76.7334	90	545	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.62	99.37	0.87	0.86	3	-
GCA_013297995.1	s__Sediminibacterium sp013297995	76.5201	91	545	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 08:43:51,920] [INFO] GTDB search result was written to GCA_947448075.1_Jr-11may16-303_genomic.fna/result_gtdb.tsv
[2023-06-13 08:43:51,920] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:43:51,923] [INFO] DFAST_QC result json was written to GCA_947448075.1_Jr-11may16-303_genomic.fna/dqc_result.json
[2023-06-13 08:43:51,924] [INFO] DFAST_QC completed!
[2023-06-13 08:43:51,924] [INFO] Total running time: 0h1m0s