[2024-01-24 12:06:10,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference
[2024-01-24 12:06:13,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,069] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,070] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a48ac8d-0d60-4c9c-87ab-f47634135867/GCF_016653465.1_ASM1665346v1_genomic.fna.gz | prodigal -d GCF_016653465.1_ASM1665346v1_genomic.fna/cds.fna -a GCF_016653465.1_ASM1665346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,387] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,388] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,388] [INFO] Running command: hmmsearch --tblout GCF_016653465.1_ASM1665346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference/reference_markers.hmm GCF_016653465.1_ASM1665346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:27,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:27,766] [INFO] Found 6/6 markers.
[2024-01-24 12:06:27,819] [INFO] Query marker FASTA was written to GCF_016653465.1_ASM1665346v1_genomic.fna/markers.fasta
[2024-01-24 12:06:27,825] [INFO] Task started: Blastn
[2024-01-24 12:06:27,825] [INFO] Running command: blastn -query GCF_016653465.1_ASM1665346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference/reference_markers.fasta -out GCF_016653465.1_ASM1665346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:28,610] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:28,614] [INFO] Selected 13 target genomes.
[2024-01-24 12:06:28,615] [INFO] Target genome list was writen to GCF_016653465.1_ASM1665346v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:28,628] [INFO] Task started: fastANI
[2024-01-24 12:06:28,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a48ac8d-0d60-4c9c-87ab-f47634135867/GCF_016653465.1_ASM1665346v1_genomic.fna.gz --refList GCF_016653465.1_ASM1665346v1_genomic.fna/target_genomes.txt --output GCF_016653465.1_ASM1665346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:43,366] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:43,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:43,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:43,383] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:43,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:43,384] [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
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	100.0	1647	1664	95	conclusive
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	90.4833	1075	1664	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	81.3113	785	1664	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	79.5485	585	1664	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	79.3925	522	1664	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	79.3784	568	1664	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	78.6864	491	1664	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.5608	489	1664	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.351	435	1664	95	below_threshold
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	77.2021	171	1664	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.6805	155	1664	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.7305	100	1664	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.553	98	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:43,389] [INFO] DFAST Taxonomy check result was written to GCF_016653465.1_ASM1665346v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:43,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:43,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:43,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference/checkm_data
[2024-01-24 12:06:43,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:43,480] [INFO] Task started: CheckM
[2024-01-24 12:06:43,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653465.1_ASM1665346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653465.1_ASM1665346v1_genomic.fna/checkm_input GCF_016653465.1_ASM1665346v1_genomic.fna/checkm_result
[2024-01-24 12:07:28,329] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:28,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:28,353] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:28,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:28,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653465.1_ASM1665346v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:28,355] [INFO] Task started: Blastn
[2024-01-24 12:07:28,355] [INFO] Running command: blastn -query GCF_016653465.1_ASM1665346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c85c763-427f-4816-a958-b39b3e94755f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653465.1_ASM1665346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:29,591] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:29,596] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:29,596] [INFO] Target genome list was writen to GCF_016653465.1_ASM1665346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:29,604] [INFO] Task started: fastANI
[2024-01-24 12:07:29,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a48ac8d-0d60-4c9c-87ab-f47634135867/GCF_016653465.1_ASM1665346v1_genomic.fna.gz --refList GCF_016653465.1_ASM1665346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653465.1_ASM1665346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:41,031] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:41,047] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:41,047] [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_016653465.1	s__Chromatium minus	100.0	1647	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903866365.1	s__Chromatium sp903866365	91.0569	1116	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227745.2	s__Chromatium violascens	90.4803	1075	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	81.3076	785	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342175.1	s__Thiobaca trueperi	80.7441	669	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	79.3874	567	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_000585215.1	s__Imhoffiella purpurea	79.3196	572	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897335.1	s__Chromatium sp903897335	79.2691	474	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	99.90	99.90	0.95	0.95	2	-
GCF_016583565.1	s__Thiorhodococcus violacea_A	79.1418	594	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	78.8159	481	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:41,049] [INFO] GTDB search result was written to GCF_016653465.1_ASM1665346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:41,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:41,055] [INFO] DFAST_QC result json was written to GCF_016653465.1_ASM1665346v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:41,055] [INFO] DFAST_QC completed!
[2024-01-24 12:07:41,055] [INFO] Total running time: 0h1m31s