[2024-01-24 12:00:36,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference
[2024-01-24 12:00:39,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,379] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg44972dfc-a9d0-4d86-b423-efa64400cbb7/GCF_018409545.1_ASM1840954v1_genomic.fna.gz | prodigal -d GCF_018409545.1_ASM1840954v1_genomic.fna/cds.fna -a GCF_018409545.1_ASM1840954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:48,955] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:48,956] [INFO] Task started: HMMsearch
[2024-01-24 12:00:48,956] [INFO] Running command: hmmsearch --tblout GCF_018409545.1_ASM1840954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference/reference_markers.hmm GCF_018409545.1_ASM1840954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:49,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:49,205] [INFO] Found 6/6 markers.
[2024-01-24 12:00:49,239] [INFO] Query marker FASTA was written to GCF_018409545.1_ASM1840954v1_genomic.fna/markers.fasta
[2024-01-24 12:00:49,239] [INFO] Task started: Blastn
[2024-01-24 12:00:49,239] [INFO] Running command: blastn -query GCF_018409545.1_ASM1840954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference/reference_markers.fasta -out GCF_018409545.1_ASM1840954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:50,100] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:50,104] [INFO] Selected 16 target genomes.
[2024-01-24 12:00:50,105] [INFO] Target genome list was writen to GCF_018409545.1_ASM1840954v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:50,121] [INFO] Task started: fastANI
[2024-01-24 12:00:50,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg44972dfc-a9d0-4d86-b423-efa64400cbb7/GCF_018409545.1_ASM1840954v1_genomic.fna.gz --refList GCF_018409545.1_ASM1840954v1_genomic.fna/target_genomes.txt --output GCF_018409545.1_ASM1840954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:03,917] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:03,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:03,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:03,932] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:01:03,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:03,932] [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
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	100.0	1126	1127	95	conclusive
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	92.6084	931	1127	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	91.0968	872	1127	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	81.0854	662	1127	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	80.3751	553	1127	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	79.8512	528	1127	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	79.6384	513	1127	95	below_threshold
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	79.3887	350	1127	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	79.0847	445	1127	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.6612	413	1127	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.6545	379	1127	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	78.0745	320	1127	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.7914	157	1127	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6979	169	1127	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.5224	145	1127	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.7723	66	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:03,935] [INFO] DFAST Taxonomy check result was written to GCF_018409545.1_ASM1840954v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:03,936] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:03,936] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:03,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference/checkm_data
[2024-01-24 12:01:03,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:03,978] [INFO] Task started: CheckM
[2024-01-24 12:01:03,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018409545.1_ASM1840954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018409545.1_ASM1840954v1_genomic.fna/checkm_input GCF_018409545.1_ASM1840954v1_genomic.fna/checkm_result
[2024-01-24 12:01:37,867] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:37,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:37,889] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:37,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:37,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018409545.1_ASM1840954v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:37,890] [INFO] Task started: Blastn
[2024-01-24 12:01:37,890] [INFO] Running command: blastn -query GCF_018409545.1_ASM1840954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg696cfc08-4e5d-4382-8f0b-3bd6888fe9fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_018409545.1_ASM1840954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:39,316] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:39,320] [INFO] Selected 9 target genomes.
[2024-01-24 12:01:39,320] [INFO] Target genome list was writen to GCF_018409545.1_ASM1840954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:39,328] [INFO] Task started: fastANI
[2024-01-24 12:01:39,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg44972dfc-a9d0-4d86-b423-efa64400cbb7/GCF_018409545.1_ASM1840954v1_genomic.fna.gz --refList GCF_018409545.1_ASM1840954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018409545.1_ASM1840954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:47,919] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:47,932] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:47,933] [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_018409545.1	s__Allochromatium tepidum	100.0	1126	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013385175.1	s__Allochromatium humboldtianum	92.6084	931	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	91.1168	871	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_009720725.1	s__Allochromatium palmeri	87.7465	840	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664085.1	s__Thermochromatium tepidum	86.2324	795	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thermochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107145.1	s__Allochromatium warmingii	79.4169	348	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583825.1	s__Thiohalocapsa halophila	78.0668	317	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	95.31	95.31	0.87	0.87	2	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	77.6886	372	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897335.1	s__Chromatium sp903897335	77.6108	281	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	99.90	99.90	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:47,935] [INFO] GTDB search result was written to GCF_018409545.1_ASM1840954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:47,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:47,940] [INFO] DFAST_QC result json was written to GCF_018409545.1_ASM1840954v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:47,940] [INFO] DFAST_QC completed!
[2024-01-24 12:01:47,940] [INFO] Total running time: 0h1m11s