[2023-06-29 09:41:30,625] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:41:30,651] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:41:30,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference
[2023-06-29 09:41:32,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:41:32,250] [INFO] Task started: Prodigal
[2023-06-29 09:41:32,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg38a51273-4ff8-477c-a6d3-c4a33a9ac385/GCA_027063075.1_ASM2706307v1_genomic.fna.gz | prodigal -d GCA_027063075.1_ASM2706307v1_genomic.fna/cds.fna -a GCA_027063075.1_ASM2706307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:41:34,024] [INFO] Task succeeded: Prodigal
[2023-06-29 09:41:34,024] [INFO] Task started: HMMsearch
[2023-06-29 09:41:34,025] [INFO] Running command: hmmsearch --tblout GCA_027063075.1_ASM2706307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference/reference_markers.hmm GCA_027063075.1_ASM2706307v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:41:34,236] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:41:34,237] [INFO] Found 6/6 markers.
[2023-06-29 09:41:34,257] [INFO] Query marker FASTA was written to GCA_027063075.1_ASM2706307v1_genomic.fna/markers.fasta
[2023-06-29 09:41:34,257] [INFO] Task started: Blastn
[2023-06-29 09:41:34,257] [INFO] Running command: blastn -query GCA_027063075.1_ASM2706307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference/reference_markers.fasta -out GCA_027063075.1_ASM2706307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:41:36,571] [INFO] Task succeeded: Blastn
[2023-06-29 09:41:36,576] [INFO] Selected 17 target genomes.
[2023-06-29 09:41:36,576] [INFO] Target genome list was writen to GCA_027063075.1_ASM2706307v1_genomic.fna/target_genomes.txt
[2023-06-29 09:41:36,579] [INFO] Task started: fastANI
[2023-06-29 09:41:36,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg38a51273-4ff8-477c-a6d3-c4a33a9ac385/GCA_027063075.1_ASM2706307v1_genomic.fna.gz --refList GCA_027063075.1_ASM2706307v1_genomic.fna/target_genomes.txt --output GCA_027063075.1_ASM2706307v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:41:40,950] [INFO] Task succeeded: fastANI
[2023-06-29 09:41:40,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:41:40,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:41:40,960] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:41:40,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:41:40,960] [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
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	79.0025	197	323	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_000170735.1	291048	291048	type	True	78.9062	200	323	95	below_threshold
Caminibacter pacificus	strain=TB6	GCA_005083985.2	1424653	1424653	type	True	78.3889	169	323	95	below_threshold
Caminibacter pacificus	strain=DSM 27783	GCA_003752135.1	1424653	1424653	type	True	78.3823	169	323	95	below_threshold
Lebetimonas natsushimae	strain=HS1857	GCA_002335445.1	1936991	1936991	type	True	78.1462	169	323	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:41:40,962] [INFO] DFAST Taxonomy check result was written to GCA_027063075.1_ASM2706307v1_genomic.fna/tc_result.tsv
[2023-06-29 09:41:40,963] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:41:40,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:41:40,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference/checkm_data
[2023-06-29 09:41:40,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:41:40,983] [INFO] Task started: CheckM
[2023-06-29 09:41:40,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027063075.1_ASM2706307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027063075.1_ASM2706307v1_genomic.fna/checkm_input GCA_027063075.1_ASM2706307v1_genomic.fna/checkm_result
[2023-06-29 09:41:54,826] [INFO] Task succeeded: CheckM
[2023-06-29 09:41:54,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:41:54,861] [INFO] ===== Completeness check finished =====
[2023-06-29 09:41:54,861] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:41:54,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027063075.1_ASM2706307v1_genomic.fna/markers.fasta)
[2023-06-29 09:41:54,862] [INFO] Task started: Blastn
[2023-06-29 09:41:54,862] [INFO] Running command: blastn -query GCA_027063075.1_ASM2706307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e7c2fd-7afe-41a1-b2db-4fe87dbcfa43/dqc_reference/reference_markers_gtdb.fasta -out GCA_027063075.1_ASM2706307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:41:55,708] [INFO] Task succeeded: Blastn
[2023-06-29 09:41:55,713] [INFO] Selected 22 target genomes.
[2023-06-29 09:41:55,714] [INFO] Target genome list was writen to GCA_027063075.1_ASM2706307v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:41:55,723] [INFO] Task started: fastANI
[2023-06-29 09:41:55,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg38a51273-4ff8-477c-a6d3-c4a33a9ac385/GCA_027063075.1_ASM2706307v1_genomic.fna.gz --refList GCA_027063075.1_ASM2706307v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027063075.1_ASM2706307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:42:02,449] [INFO] Task succeeded: fastANI
[2023-06-29 09:42:02,459] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:42:02,460] [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_005843985.1	s__Caminibacter mediatlanticus	79.0015	197	323	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Caminibacter	95.0	98.80	98.80	0.94	0.94	2	-
GCF_003752135.1	s__Cetia pacifica	78.3823	169	323	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Cetia	95.0	99.26	98.54	0.96	0.92	3	-
GCF_002335445.1	s__Lebetimonas natsushimae	78.1686	168	323	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523275.1	s__Lebetimonas sp000523275	77.4559	124	323	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	96.86	96.81	0.99	0.99	6	-
GCF_004006315.1	s__Nautilia profundicola_A	77.407	124	323	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021725.1	s__Nautilia profundicola	77.1731	133	323	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:42:02,462] [INFO] GTDB search result was written to GCA_027063075.1_ASM2706307v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:42:02,462] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:42:02,465] [INFO] DFAST_QC result json was written to GCA_027063075.1_ASM2706307v1_genomic.fna/dqc_result.json
[2023-06-29 09:42:02,466] [INFO] DFAST_QC completed!
[2023-06-29 09:42:02,466] [INFO] Total running time: 0h0m32s