[2024-01-24 14:30:16,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference
[2024-01-24 14:30:18,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,175] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg45b62f4d-eb54-4853-b402-dbca8fad83a7/GCF_002844375.1_ASM284437v1_genomic.fna.gz | prodigal -d GCF_002844375.1_ASM284437v1_genomic.fna/cds.fna -a GCF_002844375.1_ASM284437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:38,954] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:38,955] [INFO] Task started: HMMsearch
[2024-01-24 14:30:38,955] [INFO] Running command: hmmsearch --tblout GCF_002844375.1_ASM284437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference/reference_markers.hmm GCF_002844375.1_ASM284437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:39,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:39,257] [INFO] Found 6/6 markers.
[2024-01-24 14:30:39,303] [INFO] Query marker FASTA was written to GCF_002844375.1_ASM284437v1_genomic.fna/markers.fasta
[2024-01-24 14:30:39,303] [INFO] Task started: Blastn
[2024-01-24 14:30:39,303] [INFO] Running command: blastn -query GCF_002844375.1_ASM284437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference/reference_markers.fasta -out GCF_002844375.1_ASM284437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:39,978] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:39,982] [INFO] Selected 20 target genomes.
[2024-01-24 14:30:39,983] [INFO] Target genome list was writen to GCF_002844375.1_ASM284437v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:40,047] [INFO] Task started: fastANI
[2024-01-24 14:30:40,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg45b62f4d-eb54-4853-b402-dbca8fad83a7/GCF_002844375.1_ASM284437v1_genomic.fna.gz --refList GCF_002844375.1_ASM284437v1_genomic.fna/target_genomes.txt --output GCF_002844375.1_ASM284437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:58,605] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:58,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:58,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:58,618] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:58,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:58,619] [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 marina	strain=CSC3H3	GCA_002844375.1	2048283	2048283	type	True	100.0	1810	1812	95	conclusive
Thalassospira mesophila	strain=JCM 18969	GCA_002115755.1	1293891	1293891	type	True	83.4095	1260	1812	95	below_threshold
Thalassospira xiamenensis	strain=M-5	GCA_000300235.2	220697	220697	suspected-type	True	79.6776	707	1812	95	below_threshold
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	79.5208	697	1812	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	79.348	652	1812	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	79.2966	675	1812	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	79.1224	631	1812	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	79.0044	652	1812	95	below_threshold
Thalassospira alkalitolerans	strain=JCM 18968	GCA_002115745.1	1293890	1293890	type	True	78.9187	654	1812	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	78.9128	652	1812	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	78.8953	586	1812	95	below_threshold
Thalassospira lucentensis	strain=MCCC 1A00383	GCA_003326595.1	168935	168935	type	True	78.5992	590	1812	95	below_threshold
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	78.5828	604	1812	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	75.5654	50	1812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:58,620] [INFO] DFAST Taxonomy check result was written to GCF_002844375.1_ASM284437v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:58,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:58,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:58,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference/checkm_data
[2024-01-24 14:30:58,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:58,678] [INFO] Task started: CheckM
[2024-01-24 14:30:58,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002844375.1_ASM284437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002844375.1_ASM284437v1_genomic.fna/checkm_input GCF_002844375.1_ASM284437v1_genomic.fna/checkm_result
[2024-01-24 14:31:59,134] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:59,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:59,152] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:59,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:59,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002844375.1_ASM284437v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:59,153] [INFO] Task started: Blastn
[2024-01-24 14:31:59,153] [INFO] Running command: blastn -query GCF_002844375.1_ASM284437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f67b36f-a3e3-4902-9133-f8da023ca808/dqc_reference/reference_markers_gtdb.fasta -out GCF_002844375.1_ASM284437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:00,133] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:00,136] [INFO] Selected 9 target genomes.
[2024-01-24 14:32:00,136] [INFO] Target genome list was writen to GCF_002844375.1_ASM284437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:00,152] [INFO] Task started: fastANI
[2024-01-24 14:32:00,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg45b62f4d-eb54-4853-b402-dbca8fad83a7/GCF_002844375.1_ASM284437v1_genomic.fna.gz --refList GCF_002844375.1_ASM284437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002844375.1_ASM284437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:10,395] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:10,408] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:10,408] [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_002844375.1	s__Thalassospira marina	100.0	1811	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.72	97.72	0.93	0.93	2	conclusive
GCF_003326755.1	s__Thalassospira profundimaris_B	85.9381	1316	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907695.1	s__Thalassospira sp001907695	85.6308	1300	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115825.1	s__Thalassospira sp002115825	83.5343	1305	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115755.1	s__Thalassospira mesophila	83.4023	1261	1812	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	79.2966	675	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
GCF_001613805.1	s__Thalassospira lucentensis_A	79.274	730	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.23	97.17	0.91	0.86	8	-
GCF_001613795.1	s__Thalassospira sp001613795	79.0162	591	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
GCF_000763295.1	s__Thalassospira australica	78.888	587	1812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:10,409] [INFO] GTDB search result was written to GCF_002844375.1_ASM284437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:10,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:10,414] [INFO] DFAST_QC result json was written to GCF_002844375.1_ASM284437v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:10,414] [INFO] DFAST_QC completed!
[2024-01-24 14:32:10,414] [INFO] Total running time: 0h1m54s