[2024-01-25 19:39:35,734] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:35,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:35,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference
[2024-01-25 19:39:36,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:36,837] [INFO] Task started: Prodigal
[2024-01-25 19:39:36,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg4664df44-18a8-49be-a64e-586b2d26c115/GCF_000227745.2_ASM22774v3_genomic.fna.gz | prodigal -d GCF_000227745.2_ASM22774v3_genomic.fna/cds.fna -a GCF_000227745.2_ASM22774v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:49,687] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:49,687] [INFO] Task started: HMMsearch
[2024-01-25 19:39:49,687] [INFO] Running command: hmmsearch --tblout GCF_000227745.2_ASM22774v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference/reference_markers.hmm GCF_000227745.2_ASM22774v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:49,962] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:49,963] [INFO] Found 6/6 markers.
[2024-01-25 19:39:50,018] [INFO] Query marker FASTA was written to GCF_000227745.2_ASM22774v3_genomic.fna/markers.fasta
[2024-01-25 19:39:50,018] [INFO] Task started: Blastn
[2024-01-25 19:39:50,018] [INFO] Running command: blastn -query GCF_000227745.2_ASM22774v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference/reference_markers.fasta -out GCF_000227745.2_ASM22774v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:50,741] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:50,744] [INFO] Selected 15 target genomes.
[2024-01-25 19:39:50,744] [INFO] Target genome list was writen to GCF_000227745.2_ASM22774v3_genomic.fna/target_genomes.txt
[2024-01-25 19:39:50,759] [INFO] Task started: fastANI
[2024-01-25 19:39:50,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg4664df44-18a8-49be-a64e-586b2d26c115/GCF_000227745.2_ASM22774v3_genomic.fna.gz --refList GCF_000227745.2_ASM22774v3_genomic.fna/target_genomes.txt --output GCF_000227745.2_ASM22774v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:09,153] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:09,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:09,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:09,163] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:40:09,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:09,164] [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 violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	100.0	1670	1672	95	conclusive
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	90.5306	1067	1672	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	81.0715	749	1672	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	79.8389	533	1672	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	79.7637	563	1672	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	79.689	602	1672	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	79.0086	472	1672	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.8054	527	1672	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.69	503	1672	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	78.4701	497	1672	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.4184	443	1672	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.3747	511	1672	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.3798	83	1672	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.3158	111	1672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:09,165] [INFO] DFAST Taxonomy check result was written to GCF_000227745.2_ASM22774v3_genomic.fna/tc_result.tsv
[2024-01-25 19:40:09,171] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:09,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:09,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference/checkm_data
[2024-01-25 19:40:09,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:09,221] [INFO] Task started: CheckM
[2024-01-25 19:40:09,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000227745.2_ASM22774v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000227745.2_ASM22774v3_genomic.fna/checkm_input GCF_000227745.2_ASM22774v3_genomic.fna/checkm_result
[2024-01-25 19:40:47,377] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:47,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:47,407] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:47,407] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:47,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000227745.2_ASM22774v3_genomic.fna/markers.fasta)
[2024-01-25 19:40:47,408] [INFO] Task started: Blastn
[2024-01-25 19:40:47,408] [INFO] Running command: blastn -query GCF_000227745.2_ASM22774v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg66685077-89f2-417d-888b-c3ab88033b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_000227745.2_ASM22774v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:48,596] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:48,599] [INFO] Selected 10 target genomes.
[2024-01-25 19:40:48,599] [INFO] Target genome list was writen to GCF_000227745.2_ASM22774v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:48,610] [INFO] Task started: fastANI
[2024-01-25 19:40:48,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg4664df44-18a8-49be-a64e-586b2d26c115/GCF_000227745.2_ASM22774v3_genomic.fna.gz --refList GCF_000227745.2_ASM22774v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000227745.2_ASM22774v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:03,081] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:03,089] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:03,089] [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_000227745.2	s__Chromatium violascens	100.0	1670	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016653465.1	s__Chromatium minus	90.5004	1070	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	89.4641	970	1672	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	81.034	755	1672	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	80.9882	734	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	79.8064	536	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585215.1	s__Imhoffiella purpurea	79.4495	615	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583565.1	s__Thiorhodococcus violacea_A	79.2752	610	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897335.1	s__Chromatium sp903897335	79.1645	494	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	99.90	99.90	0.95	0.95	2	-
GCF_001499735.1	s__Thiocapsa sp001499735	78.9154	487	1672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:03,091] [INFO] GTDB search result was written to GCF_000227745.2_ASM22774v3_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:03,091] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:03,094] [INFO] DFAST_QC result json was written to GCF_000227745.2_ASM22774v3_genomic.fna/dqc_result.json
[2024-01-25 19:41:03,094] [INFO] DFAST_QC completed!
[2024-01-25 19:41:03,094] [INFO] Total running time: 0h1m27s