[2024-01-24 14:55:26,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference
[2024-01-24 14:55:28,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,097] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,097] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eef3b49-e331-4586-87b9-19884b2560e1/GCF_011290485.1_ASM1129048v1_genomic.fna.gz | prodigal -d GCF_011290485.1_ASM1129048v1_genomic.fna/cds.fna -a GCF_011290485.1_ASM1129048v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:37,357] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:37,358] [INFO] Task started: HMMsearch
[2024-01-24 14:55:37,358] [INFO] Running command: hmmsearch --tblout GCF_011290485.1_ASM1129048v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference/reference_markers.hmm GCF_011290485.1_ASM1129048v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:37,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:37,613] [INFO] Found 6/6 markers.
[2024-01-24 14:55:37,645] [INFO] Query marker FASTA was written to GCF_011290485.1_ASM1129048v1_genomic.fna/markers.fasta
[2024-01-24 14:55:37,646] [INFO] Task started: Blastn
[2024-01-24 14:55:37,646] [INFO] Running command: blastn -query GCF_011290485.1_ASM1129048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference/reference_markers.fasta -out GCF_011290485.1_ASM1129048v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:38,451] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:38,454] [INFO] Selected 16 target genomes.
[2024-01-24 14:55:38,455] [INFO] Target genome list was writen to GCF_011290485.1_ASM1129048v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:38,462] [INFO] Task started: fastANI
[2024-01-24 14:55:38,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eef3b49-e331-4586-87b9-19884b2560e1/GCF_011290485.1_ASM1129048v1_genomic.fna.gz --refList GCF_011290485.1_ASM1129048v1_genomic.fna/target_genomes.txt --output GCF_011290485.1_ASM1129048v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:53,520] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:53,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:53,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:53,530] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:53,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:53,531] [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
Caldichromatium japonicum	strain=No.7	GCA_011290485.1	2699430	2699430	type	True	100.0	994	996	95	conclusive
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	78.7325	404	996	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	78.5554	416	996	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.1823	398	996	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	77.4055	260	996	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.2154	258	996	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.2059	255	996	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.2016	148	996	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	77.1038	224	996	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	76.8524	190	996	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	76.8008	176	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:53,532] [INFO] DFAST Taxonomy check result was written to GCF_011290485.1_ASM1129048v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:53,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:53,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:53,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference/checkm_data
[2024-01-24 14:55:53,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:53,563] [INFO] Task started: CheckM
[2024-01-24 14:55:53,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011290485.1_ASM1129048v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011290485.1_ASM1129048v1_genomic.fna/checkm_input GCF_011290485.1_ASM1129048v1_genomic.fna/checkm_result
[2024-01-24 14:56:23,031] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:23,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,050] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:23,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:23,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011290485.1_ASM1129048v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:23,051] [INFO] Task started: Blastn
[2024-01-24 14:56:23,051] [INFO] Running command: blastn -query GCF_011290485.1_ASM1129048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f7e020c-cc43-47a4-8e64-510a7ffc19ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_011290485.1_ASM1129048v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:24,548] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:24,551] [INFO] Selected 22 target genomes.
[2024-01-24 14:56:24,552] [INFO] Target genome list was writen to GCF_011290485.1_ASM1129048v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:24,574] [INFO] Task started: fastANI
[2024-01-24 14:56:24,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eef3b49-e331-4586-87b9-19884b2560e1/GCF_011290485.1_ASM1129048v1_genomic.fna.gz --refList GCF_011290485.1_ASM1129048v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011290485.1_ASM1129048v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:44,111] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:44,127] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:44,127] [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_011290485.1	s__Caldichromatium japonicum	100.0	996	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Caldichromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013385175.1	s__Allochromatium humboldtianum	78.7221	405	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	78.5184	416	996	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	78.3851	412	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thermochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	78.1399	399	996	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	77.9935	364	996	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	77.4163	259	996	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	77.4073	235	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585215.1	s__Imhoffiella purpurea	77.2772	238	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	77.206	258	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_012276755.1	s__Marichromatium bheemlicum	77.1038	224	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224065.1	s__Imhoffiella drewsii	76.9655	207	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223985.1	s__Thiocapsa marina	76.9099	176	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583565.1	s__Thiorhodococcus violacea_A	76.8692	198	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	76.8144	175	996	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	76.7415	180	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	76.6917	214	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423035.1	s__Thiocapsa sp002423035	76.3911	154	996	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 14:56:44,131] [INFO] GTDB search result was written to GCF_011290485.1_ASM1129048v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:44,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:44,136] [INFO] DFAST_QC result json was written to GCF_011290485.1_ASM1129048v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:44,136] [INFO] DFAST_QC completed!
[2024-01-24 14:56:44,136] [INFO] Total running time: 0h1m17s