[2024-01-24 12:31:03,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference
[2024-01-24 12:31:04,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,819] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg67ededd8-463a-4a15-83ad-8a3756335099/GCF_003326595.1_ASM332659v1_genomic.fna.gz | prodigal -d GCF_003326595.1_ASM332659v1_genomic.fna/cds.fna -a GCF_003326595.1_ASM332659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:20,576] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:20,577] [INFO] Task started: HMMsearch
[2024-01-24 12:31:20,577] [INFO] Running command: hmmsearch --tblout GCF_003326595.1_ASM332659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference/reference_markers.hmm GCF_003326595.1_ASM332659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:20,944] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:20,946] [INFO] Found 6/6 markers.
[2024-01-24 12:31:20,995] [INFO] Query marker FASTA was written to GCF_003326595.1_ASM332659v1_genomic.fna/markers.fasta
[2024-01-24 12:31:20,995] [INFO] Task started: Blastn
[2024-01-24 12:31:20,995] [INFO] Running command: blastn -query GCF_003326595.1_ASM332659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference/reference_markers.fasta -out GCF_003326595.1_ASM332659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:21,769] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:21,774] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:21,775] [INFO] Target genome list was writen to GCF_003326595.1_ASM332659v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:21,798] [INFO] Task started: fastANI
[2024-01-24 12:31:21,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg67ededd8-463a-4a15-83ad-8a3756335099/GCF_003326595.1_ASM332659v1_genomic.fna.gz --refList GCF_003326595.1_ASM332659v1_genomic.fna/target_genomes.txt --output GCF_003326595.1_ASM332659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:35,106] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:35,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:35,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:35,117] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:35,118] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:31:35,118] [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
Thalassospira lucentensis	strain=MCCC 1A00383	GCA_003326595.1	168935	168935	type	True	100.0	1558	1562	95	inconclusive
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	99.9984	1556	1562	95	inconclusive
Thalassospira lohafexi	strain=139Z-12	GCA_002844275.1	744227	744227	type	True	95.8164	1383	1562	95	inconclusive
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	82.1711	1045	1562	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	82.0427	1013	1562	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	82.036	984	1562	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	82.034	1014	1562	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	81.8107	990	1562	95	below_threshold
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	81.062	907	1562	95	below_threshold
Thalassospira permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	80.8702	898	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:35,120] [INFO] DFAST Taxonomy check result was written to GCF_003326595.1_ASM332659v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:35,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:35,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:35,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference/checkm_data
[2024-01-24 12:31:35,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:35,172] [INFO] Task started: CheckM
[2024-01-24 12:31:35,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003326595.1_ASM332659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003326595.1_ASM332659v1_genomic.fna/checkm_input GCF_003326595.1_ASM332659v1_genomic.fna/checkm_result
[2024-01-24 12:32:25,206] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:25,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:25,228] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:25,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:25,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003326595.1_ASM332659v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:25,229] [INFO] Task started: Blastn
[2024-01-24 12:32:25,230] [INFO] Running command: blastn -query GCF_003326595.1_ASM332659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e68b3e-f752-437a-ab76-4ab60854919d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003326595.1_ASM332659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:26,477] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:26,481] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:26,481] [INFO] Target genome list was writen to GCF_003326595.1_ASM332659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:26,501] [INFO] Task started: fastANI
[2024-01-24 12:32:26,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg67ededd8-463a-4a15-83ad-8a3756335099/GCF_003326595.1_ASM332659v1_genomic.fna.gz --refList GCF_003326595.1_ASM332659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003326595.1_ASM332659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:39,261] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:39,277] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:39,277] [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_000421265.1	s__Thalassospira lucentensis	99.9984	1556	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	97.14	96.17	0.92	0.88	5	conclusive
GCF_002844275.1	s__Thalassospira lohafexi	95.8164	1383	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_011806425.1	s__Thalassospira lucentensis_B	84.3805	1117	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	82.2757	1003	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003326795.1	s__Thalassospira profundimaris_C	82.211	1014	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844235.1	s__Thalassospira povalilytica	82.1637	1046	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
GCF_001662875.1	s__Thalassospira tepidiphila	82.0427	1013	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_000300275.1	s__Thalassospira profundimaris	82.0212	986	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_017922435.1	s__Thalassospira sp017922435	81.9157	1031	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCA_002709775.1	s__Thalassospira sp002709775	81.8345	913	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763295.1	s__Thalassospira australica	81.8208	988	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806525.1	s__Thalassospira sp011806525	81.7099	961	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300235.2	s__Thalassospira xiamenensis	81.0212	905	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.55	97.14	0.89	0.82	23	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:39,280] [INFO] GTDB search result was written to GCF_003326595.1_ASM332659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:39,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:39,284] [INFO] DFAST_QC result json was written to GCF_003326595.1_ASM332659v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:39,284] [INFO] DFAST_QC completed!
[2024-01-24 12:32:39,284] [INFO] Total running time: 0h1m36s