[2023-06-17 16:58:58,839] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:58:58,843] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:58:58,843] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference
[2023-06-17 16:59:00,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:59:00,355] [INFO] Task started: Prodigal
[2023-06-17 16:59:00,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg69b65397-b219-4e60-829f-e1264d094e55/GCA_003526435.1_ASM352643v1_genomic.fna.gz | prodigal -d GCA_003526435.1_ASM352643v1_genomic.fna/cds.fna -a GCA_003526435.1_ASM352643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:59:13,431] [INFO] Task succeeded: Prodigal
[2023-06-17 16:59:13,432] [INFO] Task started: HMMsearch
[2023-06-17 16:59:13,432] [INFO] Running command: hmmsearch --tblout GCA_003526435.1_ASM352643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference/reference_markers.hmm GCA_003526435.1_ASM352643v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:59:13,714] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:59:13,715] [INFO] Found 6/6 markers.
[2023-06-17 16:59:13,775] [INFO] Query marker FASTA was written to GCA_003526435.1_ASM352643v1_genomic.fna/markers.fasta
[2023-06-17 16:59:13,775] [INFO] Task started: Blastn
[2023-06-17 16:59:13,775] [INFO] Running command: blastn -query GCA_003526435.1_ASM352643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference/reference_markers.fasta -out GCA_003526435.1_ASM352643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:14,392] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:14,396] [INFO] Selected 20 target genomes.
[2023-06-17 16:59:14,397] [INFO] Target genome list was writen to GCA_003526435.1_ASM352643v1_genomic.fna/target_genomes.txt
[2023-06-17 16:59:14,399] [INFO] Task started: fastANI
[2023-06-17 16:59:14,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b65397-b219-4e60-829f-e1264d094e55/GCA_003526435.1_ASM352643v1_genomic.fna.gz --refList GCA_003526435.1_ASM352643v1_genomic.fna/target_genomes.txt --output GCA_003526435.1_ASM352643v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:59:31,029] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:31,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:59:31,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:59:31,038] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:59:31,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:59:31,039] [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	81.11	588	808	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.9027	132	808	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	76.3904	97	808	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.1038	60	808	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	76.0812	103	808	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	75.9068	103	808	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	75.6673	50	808	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	75.3471	52	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:59:31,046] [INFO] DFAST Taxonomy check result was written to GCA_003526435.1_ASM352643v1_genomic.fna/tc_result.tsv
[2023-06-17 16:59:31,047] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:59:31,047] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:59:31,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference/checkm_data
[2023-06-17 16:59:31,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:59:31,084] [INFO] Task started: CheckM
[2023-06-17 16:59:31,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003526435.1_ASM352643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003526435.1_ASM352643v1_genomic.fna/checkm_input GCA_003526435.1_ASM352643v1_genomic.fna/checkm_result
[2023-06-17 17:00:11,890] [INFO] Task succeeded: CheckM
[2023-06-17 17:00:11,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 17:00:11,914] [INFO] ===== Completeness check finished =====
[2023-06-17 17:00:11,914] [INFO] ===== Start GTDB Search =====
[2023-06-17 17:00:11,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003526435.1_ASM352643v1_genomic.fna/markers.fasta)
[2023-06-17 17:00:11,915] [INFO] Task started: Blastn
[2023-06-17 17:00:11,915] [INFO] Running command: blastn -query GCA_003526435.1_ASM352643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2dba997-22c2-49d4-9f98-1ae1e31fd398/dqc_reference/reference_markers_gtdb.fasta -out GCA_003526435.1_ASM352643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:00:12,789] [INFO] Task succeeded: Blastn
[2023-06-17 17:00:12,794] [INFO] Selected 17 target genomes.
[2023-06-17 17:00:12,794] [INFO] Target genome list was writen to GCA_003526435.1_ASM352643v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 17:00:12,807] [INFO] Task started: fastANI
[2023-06-17 17:00:12,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b65397-b219-4e60-829f-e1264d094e55/GCA_003526435.1_ASM352643v1_genomic.fna.gz --refList GCA_003526435.1_ASM352643v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003526435.1_ASM352643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 17:00:23,923] [INFO] Task succeeded: fastANI
[2023-06-17 17:00:23,942] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 17:00:23,942] [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_003526435.1	s__Sediminibacterium sp003526435	100.0	786	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004361915.1	s__Sediminibacterium goheungense	81.1246	586	808	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	79.0629	352	808	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	78.6613	342	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741945.1	s__Sediminibacterium sp016741945	77.9684	233	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996675.1	s__Sediminibacterium sp009996675	77.5687	238	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167075.1	s__Sediminibacterium ginsengisoli	76.9027	132	808	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	76.8665	115	808	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	76.7139	125	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.86	97.42	0.87	0.81	7	-
GCA_016183765.1	s__Sediminibacterium sp016183765	76.6187	156	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289065.1	s__Sediminibacterium sp013289065	76.3567	74	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830285.1	s__CAILAF01 sp903830285	75.9625	67	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.59	99.53	0.91	0.89	4	-
GCF_000511175.1	s__Sediminibacterium salmoneum	75.9111	99	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884185.1	s__CAILAF01 sp903884185	75.8223	76	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.92	99.92	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-17 17:00:23,944] [INFO] GTDB search result was written to GCA_003526435.1_ASM352643v1_genomic.fna/result_gtdb.tsv
[2023-06-17 17:00:23,944] [INFO] ===== GTDB Search completed =====
[2023-06-17 17:00:23,948] [INFO] DFAST_QC result json was written to GCA_003526435.1_ASM352643v1_genomic.fna/dqc_result.json
[2023-06-17 17:00:23,948] [INFO] DFAST_QC completed!
[2023-06-17 17:00:23,948] [INFO] Total running time: 0h1m25s