[2024-01-24 13:22:17,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:17,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:17,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference
[2024-01-24 13:22:19,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:19,017] [INFO] Task started: Prodigal
[2024-01-24 13:22:19,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a399706-b6fa-4ed2-af6d-7a5d12acdf5c/GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/cds.fna -a GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:35,176] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:35,177] [INFO] Task started: HMMsearch
[2024-01-24 13:22:35,177] [INFO] Running command: hmmsearch --tblout GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference/reference_markers.hmm GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:35,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:35,574] [INFO] Found 6/6 markers.
[2024-01-24 13:22:35,632] [INFO] Query marker FASTA was written to GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:35,633] [INFO] Task started: Blastn
[2024-01-24 13:22:35,633] [INFO] Running command: blastn -query GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference/reference_markers.fasta -out GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:36,473] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:36,476] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:36,476] [INFO] Target genome list was writen to GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:36,482] [INFO] Task started: fastANI
[2024-01-24 13:22:36,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a399706-b6fa-4ed2-af6d-7a5d12acdf5c/GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna.gz --refList GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:48,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:48,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:48,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:48,523] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:48,523] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:48,524] [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 xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	100.0	1542	1543	95	inconclusive
Thalassospira xiamenensis	strain=M-5	GCA_000300235.2	220697	220697	suspected-type	True	99.9972	1542	1543	95	inconclusive
Thalassospira permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	97.8441	1358	1543	95	inconclusive
Thalassospira xianhensis	strain=MCCC 1A02616	GCA_003326475.1	478503	478503	type	True	91.0903	1246	1543	95	below_threshold
Thalassospira alkalitolerans	strain=JCM 18968	GCA_002115745.1	1293890	1293890	type	True	83.4278	1128	1543	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	81.2296	920	1543	95	below_threshold
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	80.9273	911	1543	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	76.3406	57	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:48,525] [INFO] DFAST Taxonomy check result was written to GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:48,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:48,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:48,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference/checkm_data
[2024-01-24 13:22:48,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:48,577] [INFO] Task started: CheckM
[2024-01-24 13:22:48,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/checkm_input GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:39,159] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:39,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,177] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:39,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:39,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:39,178] [INFO] Task started: Blastn
[2024-01-24 13:23:39,178] [INFO] Running command: blastn -query GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg24758cd5-e919-4f4a-b25e-f48351dd2ace/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:40,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:40,734] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:40,734] [INFO] Target genome list was writen to GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:40,768] [INFO] Task started: fastANI
[2024-01-24 13:23:40,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a399706-b6fa-4ed2-af6d-7a5d12acdf5c/GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna.gz --refList GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:49,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:49,865] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:49,865] [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_000300235.2	s__Thalassospira xiamenensis	99.9972	1542	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.55	97.14	0.89	0.82	23	conclusive
GCF_002115785.1	s__Thalassospira sp002115785	94.9286	1342	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326475.1	s__Thalassospira xianhensis	91.0903	1246	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613805.1	s__Thalassospira lucentensis_A	90.9983	1287	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.23	97.17	0.91	0.86	8	-
GCF_002115745.1	s__Thalassospira alkalitolerans	83.435	1127	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	81.2297	920	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_000421265.1	s__Thalassospira lucentensis	80.9427	910	1543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	97.14	96.17	0.92	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:49,867] [INFO] GTDB search result was written to GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:49,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:49,870] [INFO] DFAST_QC result json was written to GCF_900156715.1_IMG-taxon_2681813519_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:49,870] [INFO] DFAST_QC completed!
[2024-01-24 13:23:49,870] [INFO] Total running time: 0h1m32s