[2023-06-27 04:59:34,424] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:59:34,426] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:59:34,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference
[2023-06-27 04:59:35,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:59:35,643] [INFO] Task started: Prodigal
[2023-06-27 04:59:35,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg0430b530-84aa-44cb-8f5e-312e20460d6d/GCA_026042565.1_ASM2604256v1_genomic.fna.gz | prodigal -d GCA_026042565.1_ASM2604256v1_genomic.fna/cds.fna -a GCA_026042565.1_ASM2604256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:59:52,381] [INFO] Task succeeded: Prodigal
[2023-06-27 04:59:52,381] [INFO] Task started: HMMsearch
[2023-06-27 04:59:52,381] [INFO] Running command: hmmsearch --tblout GCA_026042565.1_ASM2604256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference/reference_markers.hmm GCA_026042565.1_ASM2604256v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:59:52,704] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:59:52,706] [INFO] Found 6/6 markers.
[2023-06-27 04:59:52,765] [INFO] Query marker FASTA was written to GCA_026042565.1_ASM2604256v1_genomic.fna/markers.fasta
[2023-06-27 04:59:52,765] [INFO] Task started: Blastn
[2023-06-27 04:59:52,765] [INFO] Running command: blastn -query GCA_026042565.1_ASM2604256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference/reference_markers.fasta -out GCA_026042565.1_ASM2604256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:59:53,359] [INFO] Task succeeded: Blastn
[2023-06-27 04:59:53,365] [INFO] Selected 34 target genomes.
[2023-06-27 04:59:53,366] [INFO] Target genome list was writen to GCA_026042565.1_ASM2604256v1_genomic.fna/target_genomes.txt
[2023-06-27 04:59:53,369] [INFO] Task started: fastANI
[2023-06-27 04:59:53,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg0430b530-84aa-44cb-8f5e-312e20460d6d/GCA_026042565.1_ASM2604256v1_genomic.fna.gz --refList GCA_026042565.1_ASM2604256v1_genomic.fna/target_genomes.txt --output GCA_026042565.1_ASM2604256v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:00:18,259] [INFO] Task succeeded: fastANI
[2023-06-27 05:00:18,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:00:18,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:00:18,271] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:00:18,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:00:18,272] [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
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.2692	63	1968	95	below_threshold
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	77.1388	108	1968	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.0882	64	1968	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.9014	55	1968	95	below_threshold
Thiolapillus brandeum	strain=Hiromi 1	GCA_000828615.1	1076588	1076588	type	True	76.8695	64	1968	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.8532	64	1968	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.8393	51	1968	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:00:18,274] [INFO] DFAST Taxonomy check result was written to GCA_026042565.1_ASM2604256v1_genomic.fna/tc_result.tsv
[2023-06-27 05:00:18,274] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:00:18,274] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:00:18,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference/checkm_data
[2023-06-27 05:00:18,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:00:18,344] [INFO] Task started: CheckM
[2023-06-27 05:00:18,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026042565.1_ASM2604256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026042565.1_ASM2604256v1_genomic.fna/checkm_input GCA_026042565.1_ASM2604256v1_genomic.fna/checkm_result
[2023-06-27 05:01:11,222] [INFO] Task succeeded: CheckM
[2023-06-27 05:01:11,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:01:11,253] [INFO] ===== Completeness check finished =====
[2023-06-27 05:01:11,253] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:01:11,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026042565.1_ASM2604256v1_genomic.fna/markers.fasta)
[2023-06-27 05:01:11,254] [INFO] Task started: Blastn
[2023-06-27 05:01:11,254] [INFO] Running command: blastn -query GCA_026042565.1_ASM2604256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826046cf-5223-4790-bb08-6b1353a7a218/dqc_reference/reference_markers_gtdb.fasta -out GCA_026042565.1_ASM2604256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:01:12,072] [INFO] Task succeeded: Blastn
[2023-06-27 05:01:12,077] [INFO] Selected 8 target genomes.
[2023-06-27 05:01:12,078] [INFO] Target genome list was writen to GCA_026042565.1_ASM2604256v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:01:12,084] [INFO] Task started: fastANI
[2023-06-27 05:01:12,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg0430b530-84aa-44cb-8f5e-312e20460d6d/GCA_026042565.1_ASM2604256v1_genomic.fna.gz --refList GCA_026042565.1_ASM2604256v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026042565.1_ASM2604256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:01:20,037] [INFO] Task succeeded: fastANI
[2023-06-27 05:01:20,049] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:01:20,050] [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	98.7553	1284	1968	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	94.699	1216	1968	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	81.8397	839	1968	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	80.3238	815	1968	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	80.3233	765	1968	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	78.1845	343	1968	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	78.0419	331	1968	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 05:01:20,058] [INFO] GTDB search result was written to GCA_026042565.1_ASM2604256v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:01:20,059] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:01:20,063] [INFO] DFAST_QC result json was written to GCA_026042565.1_ASM2604256v1_genomic.fna/dqc_result.json
[2023-06-27 05:01:20,063] [INFO] DFAST_QC completed!
[2023-06-27 05:01:20,063] [INFO] Total running time: 0h1m46s