[2023-06-27 22:54:07,280] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:54:07,282] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:54:07,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference
[2023-06-27 22:54:08,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:54:08,515] [INFO] Task started: Prodigal
[2023-06-27 22:54:08,516] [INFO] Running command: gunzip -c /var/lib/cwl/stg45f402f5-f0eb-4508-97ce-9539860af7f2/GCA_026042335.1_ASM2604233v1_genomic.fna.gz | prodigal -d GCA_026042335.1_ASM2604233v1_genomic.fna/cds.fna -a GCA_026042335.1_ASM2604233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:54:23,072] [INFO] Task succeeded: Prodigal
[2023-06-27 22:54:23,072] [INFO] Task started: HMMsearch
[2023-06-27 22:54:23,072] [INFO] Running command: hmmsearch --tblout GCA_026042335.1_ASM2604233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference/reference_markers.hmm GCA_026042335.1_ASM2604233v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:54:23,323] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:54:23,324] [INFO] Found 6/6 markers.
[2023-06-27 22:54:23,368] [INFO] Query marker FASTA was written to GCA_026042335.1_ASM2604233v1_genomic.fna/markers.fasta
[2023-06-27 22:54:23,368] [INFO] Task started: Blastn
[2023-06-27 22:54:23,368] [INFO] Running command: blastn -query GCA_026042335.1_ASM2604233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference/reference_markers.fasta -out GCA_026042335.1_ASM2604233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:54:23,964] [INFO] Task succeeded: Blastn
[2023-06-27 22:54:23,968] [INFO] Selected 33 target genomes.
[2023-06-27 22:54:23,969] [INFO] Target genome list was writen to GCA_026042335.1_ASM2604233v1_genomic.fna/target_genomes.txt
[2023-06-27 22:54:23,990] [INFO] Task started: fastANI
[2023-06-27 22:54:23,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f402f5-f0eb-4508-97ce-9539860af7f2/GCA_026042335.1_ASM2604233v1_genomic.fna.gz --refList GCA_026042335.1_ASM2604233v1_genomic.fna/target_genomes.txt --output GCA_026042335.1_ASM2604233v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:54:46,239] [INFO] Task succeeded: fastANI
[2023-06-27 22:54:46,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:54:46,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:54:46,247] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:54:46,247] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:54:46,247] [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
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	77.2734	94	1727	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.5953	69	1727	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.5647	67	1727	95	below_threshold
Thiolapillus brandeum	strain=Hiromi 1	GCA_000828615.1	1076588	1076588	type	True	76.5137	52	1727	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.5079	59	1727	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.4009	68	1727	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	75.945	55	1727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:54:46,249] [INFO] DFAST Taxonomy check result was written to GCA_026042335.1_ASM2604233v1_genomic.fna/tc_result.tsv
[2023-06-27 22:54:46,249] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:54:46,250] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:54:46,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference/checkm_data
[2023-06-27 22:54:46,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:54:46,303] [INFO] Task started: CheckM
[2023-06-27 22:54:46,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026042335.1_ASM2604233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026042335.1_ASM2604233v1_genomic.fna/checkm_input GCA_026042335.1_ASM2604233v1_genomic.fna/checkm_result
[2023-06-27 22:55:31,936] [INFO] Task succeeded: CheckM
[2023-06-27 22:55:31,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:55:31,960] [INFO] ===== Completeness check finished =====
[2023-06-27 22:55:31,960] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:55:31,961] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026042335.1_ASM2604233v1_genomic.fna/markers.fasta)
[2023-06-27 22:55:31,961] [INFO] Task started: Blastn
[2023-06-27 22:55:31,961] [INFO] Running command: blastn -query GCA_026042335.1_ASM2604233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85455101-736d-42ad-8b8b-b9ad9165c8ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_026042335.1_ASM2604233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:55:32,789] [INFO] Task succeeded: Blastn
[2023-06-27 22:55:32,793] [INFO] Selected 8 target genomes.
[2023-06-27 22:55:32,793] [INFO] Target genome list was writen to GCA_026042335.1_ASM2604233v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:55:32,795] [INFO] Task started: fastANI
[2023-06-27 22:55:32,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f402f5-f0eb-4508-97ce-9539860af7f2/GCA_026042335.1_ASM2604233v1_genomic.fna.gz --refList GCA_026042335.1_ASM2604233v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026042335.1_ASM2604233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:55:40,985] [INFO] Task succeeded: fastANI
[2023-06-27 22:55:40,992] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 22:55:40,992] [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_001715975.1	s__Thiodiazotropha endolucinida_A	98.4989	1277	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	98.81	98.44	0.92	0.86	30	conclusive
GCA_003058525.1	s__Thiodiazotropha sp003058525	94.7498	1223	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.55	99.55	0.93	0.93	2	-
GCA_003094555.1	s__Thiodiazotropha sp003094555	81.807	855	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.74	99.69	0.92	0.89	3	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	80.5621	788	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
GCA_003094535.1	s__Thiodiazotropha sp003094535	80.4605	777	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.75	99.58	0.95	0.90	13	-
GCA_003676145.1	s__Thiodiazotropha endolucinida	78.0731	358	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	-
GCA_001709035.1	s__Thiodiazotropha endoloripes_B	78.0654	341	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	-
--------------------------------------------------------------------------------
[2023-06-27 22:55:40,994] [INFO] GTDB search result was written to GCA_026042335.1_ASM2604233v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:55:40,995] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:55:40,998] [INFO] DFAST_QC result json was written to GCA_026042335.1_ASM2604233v1_genomic.fna/dqc_result.json
[2023-06-27 22:55:40,998] [INFO] DFAST_QC completed!
[2023-06-27 22:55:40,998] [INFO] Total running time: 0h1m34s