[2024-01-24 12:31:03,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,761] [INFO] DQC Reference Directory: /var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference
[2024-01-24 12:31:05,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,073] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg00cb4dbb-5d16-4212-b4d6-ac0276e05fce/GCF_002059185.1_ASM205918v1_genomic.fna.gz | prodigal -d GCF_002059185.1_ASM205918v1_genomic.fna/cds.fna -a GCF_002059185.1_ASM205918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:13,825] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:13,825] [INFO] Task started: HMMsearch
[2024-01-24 12:31:13,826] [INFO] Running command: hmmsearch --tblout GCF_002059185.1_ASM205918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference/reference_markers.hmm GCF_002059185.1_ASM205918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:14,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:14,169] [INFO] Found 6/6 markers.
[2024-01-24 12:31:14,205] [INFO] Query marker FASTA was written to GCF_002059185.1_ASM205918v1_genomic.fna/markers.fasta
[2024-01-24 12:31:14,206] [INFO] Task started: Blastn
[2024-01-24 12:31:14,206] [INFO] Running command: blastn -query GCF_002059185.1_ASM205918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference/reference_markers.fasta -out GCF_002059185.1_ASM205918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:15,018] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:15,021] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:15,022] [INFO] Target genome list was writen to GCF_002059185.1_ASM205918v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:15,030] [INFO] Task started: fastANI
[2024-01-24 12:31:15,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg00cb4dbb-5d16-4212-b4d6-ac0276e05fce/GCF_002059185.1_ASM205918v1_genomic.fna.gz --refList GCF_002059185.1_ASM205918v1_genomic.fna/target_genomes.txt --output GCF_002059185.1_ASM205918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:29,851] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:29,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:29,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:29,862] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:29,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:29,863] [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
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_002059185.1	64969	64969	type	True	100.0	1139	1145	95	conclusive
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_900167095.1	64969	64969	type	True	99.9837	1139	1145	95	conclusive
Oceanospirillum maris	strain=DSM 6286	GCA_000422865.1	64977	64977	type	True	78.3565	225	1145	95	below_threshold
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	78.3539	235	1145	95	below_threshold
Oceanospirillum sanctuarii	strain=AK56	GCA_002150805.1	1434821	1434821	type	True	78.3024	260	1145	95	below_threshold
Oceanospirillum linum	strain=ATCC 11336	GCA_001995095.2	966	966	type	True	78.1897	210	1145	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	76.4496	52	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:29,865] [INFO] DFAST Taxonomy check result was written to GCF_002059185.1_ASM205918v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:29,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:29,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:29,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference/checkm_data
[2024-01-24 12:31:29,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:29,906] [INFO] Task started: CheckM
[2024-01-24 12:31:29,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002059185.1_ASM205918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002059185.1_ASM205918v1_genomic.fna/checkm_input GCF_002059185.1_ASM205918v1_genomic.fna/checkm_result
[2024-01-24 12:32:01,642] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:01,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,670] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:01,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:01,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002059185.1_ASM205918v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:01,672] [INFO] Task started: Blastn
[2024-01-24 12:32:01,672] [INFO] Running command: blastn -query GCF_002059185.1_ASM205918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbac4b550-2843-4749-86d7-a04172127903/dqc_reference/reference_markers_gtdb.fasta -out GCF_002059185.1_ASM205918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:02,914] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:02,921] [INFO] Selected 24 target genomes.
[2024-01-24 12:32:02,921] [INFO] Target genome list was writen to GCF_002059185.1_ASM205918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:02,940] [INFO] Task started: fastANI
[2024-01-24 12:32:02,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg00cb4dbb-5d16-4212-b4d6-ac0276e05fce/GCF_002059185.1_ASM205918v1_genomic.fna.gz --refList GCF_002059185.1_ASM205918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002059185.1_ASM205918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:17,430] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:17,440] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:17,440] [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_900167095.1	s__Oceanospirillum multiglobuliferum	99.9837	1139	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000422865.1	s__Oceanospirillum maris	78.3565	225	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164585.1	s__Oceanospirillum sp014164585	78.342	209	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422425.1	s__Oceanospirillum beijerinckii	78.3316	237	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
GCF_002150805.1	s__Oceanospirillum sanctuarii	78.3024	260	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995095.2	s__Oceanospirillum linum	78.2004	212	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003858655.1	s__Amphritea balenae	76.4607	52	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:17,442] [INFO] GTDB search result was written to GCF_002059185.1_ASM205918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:17,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:17,447] [INFO] DFAST_QC result json was written to GCF_002059185.1_ASM205918v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:17,447] [INFO] DFAST_QC completed!
[2024-01-24 12:32:17,447] [INFO] Total running time: 0h1m14s