[2024-01-24 12:37:09,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,689] [INFO] DQC Reference Directory: /var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference
[2024-01-24 12:37:11,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,044] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,045] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb9bd43a-be7b-420c-a424-2d126ce41de3/GCF_017811155.1_ASM1781115v1_genomic.fna.gz | prodigal -d GCF_017811155.1_ASM1781115v1_genomic.fna/cds.fna -a GCF_017811155.1_ASM1781115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:39,172] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:39,172] [INFO] Task started: HMMsearch
[2024-01-24 12:37:39,173] [INFO] Running command: hmmsearch --tblout GCF_017811155.1_ASM1781115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference/reference_markers.hmm GCF_017811155.1_ASM1781115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:39,497] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:39,498] [INFO] Found 6/6 markers.
[2024-01-24 12:37:39,543] [INFO] Query marker FASTA was written to GCF_017811155.1_ASM1781115v1_genomic.fna/markers.fasta
[2024-01-24 12:37:39,543] [INFO] Task started: Blastn
[2024-01-24 12:37:39,543] [INFO] Running command: blastn -query GCF_017811155.1_ASM1781115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference/reference_markers.fasta -out GCF_017811155.1_ASM1781115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:40,120] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:40,126] [INFO] Selected 22 target genomes.
[2024-01-24 12:37:40,127] [INFO] Target genome list was writen to GCF_017811155.1_ASM1781115v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:40,150] [INFO] Task started: fastANI
[2024-01-24 12:37:40,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb9bd43a-be7b-420c-a424-2d126ce41de3/GCF_017811155.1_ASM1781115v1_genomic.fna.gz --refList GCF_017811155.1_ASM1781115v1_genomic.fna/target_genomes.txt --output GCF_017811155.1_ASM1781115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:58,459] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:58,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:58,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:58,471] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:58,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:58,471] [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
Lunatimonas salinarum	strain=KCTC 42988	GCA_017811155.1	1774590	1774590	type	True	100.0	1761	1761	95	conclusive
Lunatimonas lonarensis	strain=AK24	GCA_000390185.1	1232681	1232681	type	True	80.5626	623	1761	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	77.2886	156	1761	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	77.2357	51	1761	95	below_threshold
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	76.8454	199	1761	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.7991	59	1761	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	76.5596	61	1761	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	76.4929	140	1761	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	76.3249	133	1761	95	below_threshold
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	76.323	91	1761	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	76.241	142	1761	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.1099	64	1761	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	75.9269	81	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:58,473] [INFO] DFAST Taxonomy check result was written to GCF_017811155.1_ASM1781115v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:58,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:58,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:58,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference/checkm_data
[2024-01-24 12:37:58,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:58,525] [INFO] Task started: CheckM
[2024-01-24 12:37:58,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017811155.1_ASM1781115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017811155.1_ASM1781115v1_genomic.fna/checkm_input GCF_017811155.1_ASM1781115v1_genomic.fna/checkm_result
[2024-01-24 12:39:14,750] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:14,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:14,775] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:14,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:14,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017811155.1_ASM1781115v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:14,776] [INFO] Task started: Blastn
[2024-01-24 12:39:14,776] [INFO] Running command: blastn -query GCF_017811155.1_ASM1781115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga313618b-cbdf-4ea1-8de9-073b5b22e7c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017811155.1_ASM1781115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:15,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:15,545] [INFO] Selected 22 target genomes.
[2024-01-24 12:39:15,546] [INFO] Target genome list was writen to GCF_017811155.1_ASM1781115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:15,581] [INFO] Task started: fastANI
[2024-01-24 12:39:15,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb9bd43a-be7b-420c-a424-2d126ce41de3/GCF_017811155.1_ASM1781115v1_genomic.fna.gz --refList GCF_017811155.1_ASM1781115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017811155.1_ASM1781115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:32,945] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:32,962] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:32,962] [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_017811155.1	s__Lunatimonas salinarum	100.0	1761	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000390185.1	s__Lunatimonas lonarensis	80.5892	619	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467825.1	s__Cyclobacterium xiamenense	77.2522	158	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCF_000295935.2	s__Indibacter alkaliphilus	77.0362	58	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260975.1	s__Echinicola strongylocentroti	76.5717	66	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254835.1	s__Algoriphagus aestuariicola	76.5596	61	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	76.3709	134	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254915.1	s__Algoriphagus sp017254915	76.3497	64	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	76.3289	137	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050135.1	s__Cyclobacterium amurskyense	76.3219	91	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	76.3143	134	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	76.2286	143	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281475.1	s__Echinicola rosea	76.1799	79	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000427295.1	s__Cyclobacterium qasimii	75.9269	81	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:32,964] [INFO] GTDB search result was written to GCF_017811155.1_ASM1781115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:32,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:32,969] [INFO] DFAST_QC result json was written to GCF_017811155.1_ASM1781115v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:32,969] [INFO] DFAST_QC completed!
[2024-01-24 12:39:32,970] [INFO] Total running time: 0h2m23s