[2023-06-18 12:30:19,059] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:30:19,071] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:30:19,071] [INFO] DQC Reference Directory: /var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference
[2023-06-18 12:30:20,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:30:20,417] [INFO] Task started: Prodigal
[2023-06-18 12:30:20,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf6025af-7572-4418-8e9e-8ae07ea30183/GCA_018659485.1_ASM1865948v1_genomic.fna.gz | prodigal -d GCA_018659485.1_ASM1865948v1_genomic.fna/cds.fna -a GCA_018659485.1_ASM1865948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:30:25,439] [INFO] Task succeeded: Prodigal
[2023-06-18 12:30:25,439] [INFO] Task started: HMMsearch
[2023-06-18 12:30:25,439] [INFO] Running command: hmmsearch --tblout GCA_018659485.1_ASM1865948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference/reference_markers.hmm GCA_018659485.1_ASM1865948v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:30:25,678] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:30:25,680] [INFO] Found 6/6 markers.
[2023-06-18 12:30:25,703] [INFO] Query marker FASTA was written to GCA_018659485.1_ASM1865948v1_genomic.fna/markers.fasta
[2023-06-18 12:30:25,704] [INFO] Task started: Blastn
[2023-06-18 12:30:25,704] [INFO] Running command: blastn -query GCA_018659485.1_ASM1865948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference/reference_markers.fasta -out GCA_018659485.1_ASM1865948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:30:26,347] [INFO] Task succeeded: Blastn
[2023-06-18 12:30:26,352] [INFO] Selected 32 target genomes.
[2023-06-18 12:30:26,353] [INFO] Target genome list was writen to GCA_018659485.1_ASM1865948v1_genomic.fna/target_genomes.txt
[2023-06-18 12:30:26,364] [INFO] Task started: fastANI
[2023-06-18 12:30:26,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf6025af-7572-4418-8e9e-8ae07ea30183/GCA_018659485.1_ASM1865948v1_genomic.fna.gz --refList GCA_018659485.1_ASM1865948v1_genomic.fna/target_genomes.txt --output GCA_018659485.1_ASM1865948v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:30:49,475] [INFO] Task succeeded: fastANI
[2023-06-18 12:30:49,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:30:49,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:30:49,481] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:30:49,481] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 12:30:49,481] [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
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.0709	56	516	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	75.9787	60	516	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.9695	65	516	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 12:30:49,483] [INFO] DFAST Taxonomy check result was written to GCA_018659485.1_ASM1865948v1_genomic.fna/tc_result.tsv
[2023-06-18 12:30:49,487] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:30:49,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:30:49,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference/checkm_data
[2023-06-18 12:30:49,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:30:49,528] [INFO] Task started: CheckM
[2023-06-18 12:30:49,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018659485.1_ASM1865948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018659485.1_ASM1865948v1_genomic.fna/checkm_input GCA_018659485.1_ASM1865948v1_genomic.fna/checkm_result
[2023-06-18 12:31:11,917] [INFO] Task succeeded: CheckM
[2023-06-18 12:31:11,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:31:11,949] [INFO] ===== Completeness check finished =====
[2023-06-18 12:31:11,950] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:31:11,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018659485.1_ASM1865948v1_genomic.fna/markers.fasta)
[2023-06-18 12:31:11,951] [INFO] Task started: Blastn
[2023-06-18 12:31:11,951] [INFO] Running command: blastn -query GCA_018659485.1_ASM1865948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5af097f-369f-4f19-86bc-0cebc940e102/dqc_reference/reference_markers_gtdb.fasta -out GCA_018659485.1_ASM1865948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:12,810] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:12,814] [INFO] Selected 24 target genomes.
[2023-06-18 12:31:12,814] [INFO] Target genome list was writen to GCA_018659485.1_ASM1865948v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:31:12,841] [INFO] Task started: fastANI
[2023-06-18 12:31:12,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf6025af-7572-4418-8e9e-8ae07ea30183/GCA_018659485.1_ASM1865948v1_genomic.fna.gz --refList GCA_018659485.1_ASM1865948v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018659485.1_ASM1865948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:31:24,830] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:24,850] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:31:24,851] [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
GCA_018671895.1	s__JABHGV01 sp018671895	99.8237	484	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABHGV01	95.0	99.83	99.79	0.94	0.93	6	conclusive
GCA_013204045.1	s__JABMOQ01 sp013204045	77.6452	139	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABMOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018662005.1	s__JACNJU01 sp018662005	76.91	122	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JACNJU01	95.0	99.95	99.92	0.95	0.94	5	-
GCA_014382375.1	s__JACNJU01 sp014382375	76.6156	124	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JACNJU01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_002696205.1	s__UBA1479 sp002696205	76.4979	61	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776705.1	s__JADHSW01 sp016776705	76.4287	85	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JADHSW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845145.1	s__TMED8 sp016845145	76.2599	50	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__TMED8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.2171	65	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	76.1909	91	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002325375.1	s__UBA1479 sp002325375	76.0638	73	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_016187325.1	s__JACPJY01 sp016187325	75.8414	50	516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:31:24,853] [INFO] GTDB search result was written to GCA_018659485.1_ASM1865948v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:31:24,854] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:31:24,862] [INFO] DFAST_QC result json was written to GCA_018659485.1_ASM1865948v1_genomic.fna/dqc_result.json
[2023-06-18 12:31:24,862] [INFO] DFAST_QC completed!
[2023-06-18 12:31:24,862] [INFO] Total running time: 0h1m6s