[2024-01-24 12:15:20,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference
[2024-01-24 12:15:21,983] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:21,985] [INFO] Task started: Prodigal
[2024-01-24 12:15:21,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e579f01-ae97-4280-a896-af2e145307f4/GCF_016583985.1_ASM1658398v1_genomic.fna.gz | prodigal -d GCF_016583985.1_ASM1658398v1_genomic.fna/cds.fna -a GCF_016583985.1_ASM1658398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:36,571] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:36,572] [INFO] Task started: HMMsearch
[2024-01-24 12:15:36,572] [INFO] Running command: hmmsearch --tblout GCF_016583985.1_ASM1658398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference/reference_markers.hmm GCF_016583985.1_ASM1658398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:36,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:36,878] [INFO] Found 6/6 markers.
[2024-01-24 12:15:36,927] [INFO] Query marker FASTA was written to GCF_016583985.1_ASM1658398v1_genomic.fna/markers.fasta
[2024-01-24 12:15:36,928] [INFO] Task started: Blastn
[2024-01-24 12:15:36,928] [INFO] Running command: blastn -query GCF_016583985.1_ASM1658398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference/reference_markers.fasta -out GCF_016583985.1_ASM1658398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:37,599] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:37,603] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:37,603] [INFO] Target genome list was writen to GCF_016583985.1_ASM1658398v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:37,611] [INFO] Task started: fastANI
[2024-01-24 12:15:37,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e579f01-ae97-4280-a896-af2e145307f4/GCF_016583985.1_ASM1658398v1_genomic.fna.gz --refList GCF_016583985.1_ASM1658398v1_genomic.fna/target_genomes.txt --output GCF_016583985.1_ASM1658398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:52,694] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:52,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:52,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:52,712] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:52,712] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:52,712] [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
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	79.911	555	1506	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	79.0796	504	1506	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	78.5813	468	1506	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.4165	475	1506	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.6795	267	1506	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.6699	262	1506	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.583	255	1506	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.51	261	1506	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	77.5064	266	1506	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	77.4658	271	1506	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	77.1164	268	1506	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.9716	185	1506	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	75.827	50	1506	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	75.6889	53	1506	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	75.5753	51	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:52,714] [INFO] DFAST Taxonomy check result was written to GCF_016583985.1_ASM1658398v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:52,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:52,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:52,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference/checkm_data
[2024-01-24 12:15:52,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:52,760] [INFO] Task started: CheckM
[2024-01-24 12:15:52,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583985.1_ASM1658398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583985.1_ASM1658398v1_genomic.fna/checkm_input GCF_016583985.1_ASM1658398v1_genomic.fna/checkm_result
[2024-01-24 12:16:36,617] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:36,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:36,664] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:36,665] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:36,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583985.1_ASM1658398v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:36,666] [INFO] Task started: Blastn
[2024-01-24 12:16:36,666] [INFO] Running command: blastn -query GCF_016583985.1_ASM1658398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d76567f-4669-43bc-a1e7-86ca782b9dac/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583985.1_ASM1658398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:37,614] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:37,619] [INFO] Selected 19 target genomes.
[2024-01-24 12:16:37,619] [INFO] Target genome list was writen to GCF_016583985.1_ASM1658398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:37,671] [INFO] Task started: fastANI
[2024-01-24 12:16:37,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e579f01-ae97-4280-a896-af2e145307f4/GCF_016583985.1_ASM1658398v1_genomic.fna.gz --refList GCF_016583985.1_ASM1658398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583985.1_ASM1658398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:55,479] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:55,494] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:55,495] [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_016583985.1	s__Thiocapsa imhoffii	100.0	1502	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003634315.1	s__Thiocapsa rosea	79.9017	552	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	79.7177	528	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCF_900106925.1	s__Thiocapsa roseopersicina	79.0709	505	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	78.8005	496	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223985.1	s__Thiocapsa marina	78.5815	468	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390875.1	s__Thiocapsa sp011390875	78.4768	375	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423035.1	s__Thiocapsa sp002423035	78.3978	422	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	77.5064	266	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	77.4562	272	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_004342175.1	s__Thiobaca trueperi	77.4141	241	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	77.2956	251	1506	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	77.089	271	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828115.1	s__Thiodictyon sp903828115	77.0468	219	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938795.1	s__Marichromatium sp016938795	77.008	169	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:55,500] [INFO] GTDB search result was written to GCF_016583985.1_ASM1658398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:55,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:55,503] [INFO] DFAST_QC result json was written to GCF_016583985.1_ASM1658398v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:55,504] [INFO] DFAST_QC completed!
[2024-01-24 12:16:55,504] [INFO] Total running time: 0h1m35s