[2024-01-24 13:09:29,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,119] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference
[2024-01-24 13:09:30,349] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,350] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,350] [INFO] Running command: gunzip -c /var/lib/cwl/stg2644c853-1a4f-4b39-957b-5dfc2968f6a5/GCF_000224065.1_ASM22406v1_genomic.fna.gz | prodigal -d GCF_000224065.1_ASM22406v1_genomic.fna/cds.fna -a GCF_000224065.1_ASM22406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:45,546] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:45,547] [INFO] Task started: HMMsearch
[2024-01-24 13:09:45,547] [INFO] Running command: hmmsearch --tblout GCF_000224065.1_ASM22406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference/reference_markers.hmm GCF_000224065.1_ASM22406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:45,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:45,932] [INFO] Found 6/6 markers.
[2024-01-24 13:09:45,980] [INFO] Query marker FASTA was written to GCF_000224065.1_ASM22406v1_genomic.fna/markers.fasta
[2024-01-24 13:09:45,980] [INFO] Task started: Blastn
[2024-01-24 13:09:45,981] [INFO] Running command: blastn -query GCF_000224065.1_ASM22406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference/reference_markers.fasta -out GCF_000224065.1_ASM22406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:46,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:46,865] [INFO] Selected 17 target genomes.
[2024-01-24 13:09:46,866] [INFO] Target genome list was writen to GCF_000224065.1_ASM22406v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:46,873] [INFO] Task started: fastANI
[2024-01-24 13:09:46,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg2644c853-1a4f-4b39-957b-5dfc2968f6a5/GCF_000224065.1_ASM22406v1_genomic.fna.gz --refList GCF_000224065.1_ASM22406v1_genomic.fna/target_genomes.txt --output GCF_000224065.1_ASM22406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:01,562] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:01,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:01,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:01,581] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:01,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:01,582] [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
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	80.1369	696	1772	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	80.0234	568	1772	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	79.9937	539	1772	95	below_threshold
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	79.9621	604	1772	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	79.8878	574	1772	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	79.8561	675	1772	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	79.5161	512	1772	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	79.4891	542	1772	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	79.4302	549	1772	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	79.3114	607	1772	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	78.9854	545	1772	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	78.2837	486	1772	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.2599	429	1772	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.6312	156	1772	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.3075	146	1772	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2589	128	1772	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.4371	54	1772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:01,584] [INFO] DFAST Taxonomy check result was written to GCF_000224065.1_ASM22406v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:01,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:01,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:01,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference/checkm_data
[2024-01-24 13:10:01,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:01,646] [INFO] Task started: CheckM
[2024-01-24 13:10:01,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000224065.1_ASM22406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000224065.1_ASM22406v1_genomic.fna/checkm_input GCF_000224065.1_ASM22406v1_genomic.fna/checkm_result
[2024-01-24 13:10:49,531] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:49,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:49,553] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:49,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:49,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000224065.1_ASM22406v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:49,554] [INFO] Task started: Blastn
[2024-01-24 13:10:49,554] [INFO] Running command: blastn -query GCF_000224065.1_ASM22406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1012c15-5a61-4d84-b325-08a9a329bb8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000224065.1_ASM22406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:50,769] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:50,773] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:50,773] [INFO] Target genome list was writen to GCF_000224065.1_ASM22406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:50,783] [INFO] Task started: fastANI
[2024-01-24 13:10:50,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg2644c853-1a4f-4b39-957b-5dfc2968f6a5/GCF_000224065.1_ASM22406v1_genomic.fna.gz --refList GCF_000224065.1_ASM22406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000224065.1_ASM22406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:03,623] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:03,638] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:03,639] [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_000224065.1	s__Imhoffiella drewsii	100.0	1770	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000585215.1	s__Imhoffiella purpurea	84.5035	1086	1772	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	80.2047	717	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	80.1295	696	1772	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	80.0007	572	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_018409545.1	s__Allochromatium tepidum	79.9924	541	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	79.8925	574	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	79.8596	675	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	79.4057	554	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_016653465.1	s__Chromatium minus	78.9979	544	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664085.1	s__Thermochromatium tepidum	78.4543	424	1772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thermochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	78.2843	487	1772	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	78.2145	344	1772	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 13:11:03,642] [INFO] GTDB search result was written to GCF_000224065.1_ASM22406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:03,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:03,650] [INFO] DFAST_QC result json was written to GCF_000224065.1_ASM22406v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:03,651] [INFO] DFAST_QC completed!
[2024-01-24 13:11:03,651] [INFO] Total running time: 0h1m35s